3JTJ | pdb_00003jtj

3-deoxy-manno-octulosonate cytidylyltransferase from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3JTJ/pdb

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


• Deposited: 2009-09-12 Released: 2009-09-22 
• Deposition Author(s): Osipiuk, J., Zhou, M., Grimshaw, S., 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: 2.18 Å
• R-Value Free: 
  0.209 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

X-ray crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Yersinia pestis.

Osipiuk, J., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 28.06 kDa 
• Atom Count: 2,049 
• Modeled Residue Count: 249 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-deoxy-manno-octulosonate cytidylyltransferase	A	253	Yersinia pestis CO92	Mutation(s): 0  Gene Names: kdsB, y2772, YPO1400, YP_1193 EC: 2.7.7.38
UniProt
Find proteins for Q8ZGA4 (Yersinia pestis) Explore Q8ZGA4  Go to UniProtKB:  Q8ZGA4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	B [auth A], C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

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: 2.18 Å
• R-Value Free:  0.209 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33jtj

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.058	α = 90
b = 97.058	β = 90
c = 93.626	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Osipiuk, J., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary