3PYZ | pdb_00003pyz

Crystal structure of bifunctional folylpolyglutamate synthase/dihydrofolate synthase complexed with AMPPNP and Mn ion from Yersinia pestis c092

• PDB DOI: https://doi.org/10.2210/pdb3PYZ/pdb

• Classification: LIGASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-12-13 Released: 2011-01-19 
• Deposition Author(s): Nocek, B., Makowska-Grzyska, M., Maltseva, N., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of bifunctional folylpolyglutamate synthase/dihydrofolate synthase complexed with AMPpnp and Mn ion from Yersinia pestis c092

Nocek, B., Makowska-Grzyska, M., Maltseva, N., Anderson, W., 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)

Macromolecule Content 

• Total Structure Weight: 48.11 kDa 
• Atom Count: 3,225 
• Modeled Residue Count: 410 
• Deposited Residue Count: 437 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional folylpolyglutamate synthase/dihydrofolate synthase	A	437	Yersinia pestis CO92	Mutation(s): 0  Gene Names: folC, YPN_2178, YP516_2438 EC: 6.3.2.12 (PDB Primary Data), 6.3.2.17 (PDB Primary Data)
UniProt
Find proteins for Q8D0U0 (Yersinia pestis) Explore Q8D0U0  Go to UniProtKB:  Q8D0U0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33pyz

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.627	α = 90
b = 77.713	β = 90
c = 122.292	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
CCP4	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Nocek, B., Makowska-Grzyska, M., Maltseva, N., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-01-19
  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