3RF0 | pdb_00003rf0

Crystal Structure of Exopolyphosphatase from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3RF0/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-05 Released: 2011-04-27 
• Deposition Author(s): Kim, Y., Zhou, M., Hasseman, J., 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: 1.80 Å
• R-Value Free: 
  0.228 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Exopolyphosphatase from Yersinia pestis

Kim, Y., Zhou, M., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.75 kDa 
• Atom Count: 4,101 
• Modeled Residue Count: 397 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exopolyphosphatase	A, B	209	Yersinia pestis CO92	Mutation(s): 0  Gene Names: ppx, y1397, YPO2837, YP_2704 EC: 3.6.1.11
UniProt
Find proteins for A0A5P8YHM7 (Yersinia pestis) Explore A0A5P8YHM7  Go to UniProtKB:  A0A5P8YHM7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	C [auth A], E [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-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: 1.80 Å
• R-Value Free:  0.228 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33rf0

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.412	α = 90
b = 71.083	β = 118.29
c = 60.195	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Kim, Y., Zhou, M., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary