3LLU | pdb_00003llu

Crystal structure of the nucleotide-binding domain of Ras-related GTP-binding protein C

• PDB DOI: https://doi.org/10.2210/pdb3LLU/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-01-29 Released: 2010-02-09 
• Deposition Author(s): Nedyalkova, L., Tempel, W., Tong, Y., Crombet, L., Zhong, N., Guan, X., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.181 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the nucleotide-binding domain of Ras-related GTP-binding protein C

Nedyalkova, L., Tempel, W., Tong, Y., Crombet, L., Zhong, N., Guan, X., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.44 kDa 
• Atom Count: 1,643 
• Modeled Residue Count: 177 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related GTP-binding protein C	A	196	Homo sapiens	Mutation(s): 0  Gene Names: RRAGC EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HB90 (Homo sapiens) Explore Q9HB90  Go to UniProtKB:  Q9HB90
PHAROS:  Q9HB90 GTEx:  ENSG00000116954

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.181 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.22	α = 90
b = 72.22	β = 90
c = 72.182	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Nedyalkova, L., Tempel, W., Tong, Y., Crombet, L., Zhong, N., Guan, X., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description