5UI9 | pdb_00005ui9

Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, 2 -hydroxy-2-hydroxymethyl propanoic acid and Magnesium

PDB DOI: https://doi.org/10.2210/pdb5UI9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhizobium rhizogenes K84
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-01-13 Released: 2017-02-01
Deposition Author(s): Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.202 (Depositor), 0.220 (DCC)
R-Value Work:
0.183 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, 2 -hydroxy-2-hydroxymethyl propanoic acid and Magnesium

Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 76.59 kDa
Atom Count: 5,496
Modelled Residue Count: 684
Deposited Residue Count: 690
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase protein	A, B	345	Rhizobium rhizogenes K84	Mutation(s): 0 Gene Names: Arad_9238 EC: 1.1.1.420
UniProt
Find proteins for B9JK80 (Rhizobium rhizogenes (strain K84 / ATCC BAA-868)) Explore B9JK80 Go to UniProtKB: B9JK80
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9JK80
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
8A1 Query on 8A1 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	(2S)-2,3-dihydroxy-2-methylpropanoic acid C₄ H₈ O₄ DGADNPLBVRLJGD-BYPYZUCNSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.202 (Depositor), 0.220 (DCC)
R-Value Work: 0.183 (Depositor), 0.190 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.881	α = 90
b = 112.771	β = 94.7
c = 65.371	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118303

Revision History (Full details and data files)

Version 1.0: 2017-02-01
Type: Initial release
Version 1.1: 2017-06-07
Changes: Structure summary
Version 1.2: 2017-09-20
Changes: Author supporting evidence
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description

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Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, 2 -hydroxy-2-hydroxymethyl propanoic acid and Magnesium

Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, 2 -hydroxy-2-hydroxymethyl propanoic acid and Magnesium

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

5UI9 | pdb_00005ui9