2QTH | pdb_00002qth

Crystal structure of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb2QTH/pdb

Classification: NUCLEOTIDE BINDING PROTEIN
Organism(s): Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-08-02 Released: 2008-08-19
Deposition Author(s): Wu, H., Sun, L., Brouns, S.J., Fu, S., Rao, Z., Van der Oost, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.264 (Depositor)
R-Value Work:
0.224 (Depositor), 0.220 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus.

Wu, H., Sun, L., Brouns, S.J., Fu, S., Akerboom, J., Li, X., Zhang, C., Rao, Z., Van der Oost, J.

To be published.

Macromolecule Content

Total Structure Weight: 42.76 kDa
Atom Count: 2,686
Modelled Residue Count: 311
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein	A	364	N/A	Mutation(s): 0 Gene Names: hflX, SSO0269
UniProt
Find proteins for Q980M3 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q980M3 Go to UniProtKB: Q980M3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q980M3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	G [auth A], I [auth A], J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264 (Depositor)
R-Value Work: 0.224 (Depositor), 0.220 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.991	α = 90
b = 72.403	β = 90
c = 96.016	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
SHARP	phasing
DM	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-08-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-08-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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Crystal structure of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus in complex with GDP

Crystal structure of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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