4IQD | pdb_00004iqd

Crystal Structure of Carboxyvinyl-Carboxyphosphonate Phosphorylmutase from Bacillus anthracis

• PDB DOI: https://doi.org/10.2210/pdb4IQD/pdb
• Entry: 4IQD supersedes: 3IH1

• Classification: LYASE
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-01-11 Released: 2013-01-23 
• Deposition Author(s): Kim, Y., Maltseva, N., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.142 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Literature

Crystal Structure of Carboxyvinyl-Carboxyphosphonate Phosphorylmutase from Bacillus anthracis

Kim, Y., Maltseva, N., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.74 kDa 
• Atom Count: 4,876 
• Modeled Residue Count: 579 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxyvinyl-carboxyphosphonate phosphorylmutase	A, B	305	Bacillus anthracis	Mutation(s): 0  Gene Names: prpB, yqiQ EC: 4.1.3.30
UniProt
Find proteins for A0A6L7HJ56 (Bacillus anthracis) Explore A0A6L7HJ56  Go to UniProtKB:  A0A6L7HJ56

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYR	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.142 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34iqd

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.543	α = 90
b = 105.543	β = 90
c = 114.684	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Kim, Y., Maltseva, N., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 3IH1

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2014-12-03
  Changes: Structure summary
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-10-16
  Changes: Structure summary