1VR8 | pdb_00001vr8

Crystal structure of GTP binding regulator (TM1622) from Thermotoga Maritima at 1.75 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VR8/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-02-16 Released: 2005-03-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p.

Xu, Q., Krishna, S.S., McMullan, D., Schwarzenbacher, R., Miller, M.D., Abdubek, P., Agarwalla, S., Ambing, E., Astakhova, T., Axelrod, H.L., Canaves, J.M., Carlton, D., Chiu, H.J., Clayton, T., DiDonato, M., Duan, L., Elsliger, M.A., Feuerhelm, J., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Koesema, E., Kreusch, A., Kuhn, P., Morse, A.T., Nigoghossian, E., Okach, L., Oommachen, S., Paulsen, J., Quijano, K., Reyes, R., Rife, C.L., Spraggon, G., Stevens, R.C., van den Bedem, H., White, A., Wolf, G., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2006) Proteins 65: 777-782

• PubMed: 16948158 
• DOI: https://doi.org/10.1002/prot.21015
• Primary Citation of Related Structures:  
  1VR8

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Organizational Affiliation: 
• Joint Center for Structural Genomics.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.16 kDa 
• Atom Count: 1,305 
• Modeled Residue Count: 135 
• Deposited Residue Count: 142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP binding regulator	A	142	Thermotoga maritima	Mutation(s): 3  Gene Names: TM1622
UniProt
Find proteins for Q9X1V7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1V7  Go to UniProtKB:  Q9X1V7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
AZI	B [auth A], C [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VR8

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.73	α = 90
b = 57.73	β = 90
c = 87.944	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
autoSHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-03-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Data collection, Structure summary