4ZJM | pdb_00004zjm

Crystal Structure of Mycobacterium tuberculosis LpqH (Rv3763)

PDB DOI: https://doi.org/10.2210/pdb4ZJM/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli #1/H766
Mutation(s): No

Deposited: 2015-04-29 Released: 2015-05-13
Deposition Author(s): Arbing, M.A., Chan, S., Kuo, E., Harris, L.R., Zhou, T.T., Eisenberg, D., TB Structural Genomics Consortium (TBSGC)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Mycobacterium tuberculosis LpqH (Rv3763)

Arbing, M.A., Chan, S., Kuo, E., Harris, L.R., Zhou, T.T., Eisenberg, D.

To be published.

Macromolecule Content

Total Structure Weight: 85.29 kDa
Atom Count: 5,496
Modelled Residue Count: 784
Deposited Residue Count: 833
Unique protein chains: 7

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein LpqH	A	119	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: lpqH, Rv3763, MTV025.111
UniProt
Find proteins for P9WK61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK61 Go to UniProtKB: P9WK61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WK61
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein LpqH	B	119	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: lpqH, Rv3763, MTV025.111
UniProt
Find proteins for P9WK61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK61 Go to UniProtKB: P9WK61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WK61
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein LpqH	C	119	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: lpqH, Rv3763, MTV025.111
UniProt
Find proteins for P9WK61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK61 Go to UniProtKB: P9WK61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WK61
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein LpqH	D	119	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: lpqH, Rv3763, MTV025.111
UniProt
Find proteins for P9WK61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK61 Go to UniProtKB: P9WK61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WK61
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein LpqH	E	119	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: lpqH, Rv3763, MTV025.111
UniProt
Find proteins for P9WK61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK61 Go to UniProtKB: P9WK61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WK61
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein LpqH	F	119	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: lpqH, Rv3763, MTV025.111
UniProt
Find proteins for P9WK61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK61 Go to UniProtKB: P9WK61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WK61
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein LpqH	G	119	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: lpqH, Rv3763, MTV025.111
UniProt
Find proteins for P9WK61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK61 Go to UniProtKB: P9WK61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WK61
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth F] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth G]	AA [auth G] BA [auth G] H [auth A] I [auth A] L [auth B] AA [auth G], BA [auth G], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], T [auth D], V [auth E], W [auth E], X [auth F], Y [auth F], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B]	J [auth A], K [auth A], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.246 (Depositor), 0.250 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.37	α = 90
b = 100.37	β = 90
c = 239.15	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MR-Rosetta	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2015-05-13

Deposition Author(s):

TB Structural Genomics Consortium (TBSGC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	23616-002-06 F3:02
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	TBSGC R01 (A1068135)
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	TBSGC P01 (AI095208)

Revision History (Full details and data files)

Version 1.0: 2015-05-13
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description

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Crystal Structure of Mycobacterium tuberculosis LpqH (Rv3763)

Crystal Structure of Mycobacterium tuberculosis LpqH (Rv3763)

Entity ID: 1

UniProt

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

4ZJM | pdb_00004zjm