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.

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Experimental Data Snapshot

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

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	H [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
CD	B [auth A], C [auth A], D [auth A], E [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
ACT	G [auth A], I [auth A], J [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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), 0.224 (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

Entry History 

Deposition Data

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

Revision History  

• 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