1VK3 | pdb_00001vk3

Crystal structure of Phosphoribosylformylglycinamidine synthase II (TM1246) from Thermotoga maritima at 2.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VK3/pdb

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


• Deposited: 2004-04-23 Released: 2004-05-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution.

Mathews, I.I., Krishna, S.S., Schwarzenbacher, R., McMullan, D., Abdubek, P., Ambing, E., Canaves, J.M., Chiu, H.J., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Jaroszewski, L., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., Miller, M.D., Moy, K., Nigoghossian, E., Paulsen, J., Quijano, K., Reyes, R., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2006) Proteins 63: 1106-1111

• PubMed: 16544324 
• DOI: https://doi.org/10.1002/prot.20650
• Primary Citation Related Structures: 
  1VK3

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Organizational Affiliation: 
• Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.34 kDa 
• Atom Count: 4,666 
• Modeled Residue Count: 586 
• Deposited Residue Count: 615 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylformylglycinamidine synthase II	A	615	Thermotoga maritima	Mutation(s): 17  Gene Names: PURL, TM1246 EC: 6.3.5.3
UniProt
Find proteins for Q9X0X3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0X3  Go to UniProtKB:  Q9X0X3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.15 Å
• R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VK3

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.775	α = 90
b = 72.689	β = 90
c = 128.418	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-05-11
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary