3N4K | pdb_00003n4k

Putative RNA methyltransferase from Yersinia pestis in complex with S-ADENOSYL-L-HOMOCYSTEINE.

• PDB DOI: https://doi.org/10.2210/pdb3N4K/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-21 Released: 2010-06-23 
• Deposition Author(s): Osipiuk, J., Maltseva, N., Peterson, 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: 1.76 Å
• R-Value Free: 
  0.193 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of putative RNA methyltransferase from Yersinia pestis.

Osipiuk, J., Maltseva, N., Peterson, 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: 37.44 kDa 
• Atom Count: 2,960 
• Modeled Residue Count: 324 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA methyltransferase	A, B	165	Yersinia pestis CO92	Mutation(s): 0  Gene Names: cspR, YPO0071, YP_0071 EC: 2.1.1.207
UniProt
Find proteins for Q74Y93 (Yersinia pestis) Explore Q74Y93  Go to UniProtKB:  Q74Y93

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.193 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33n4k

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.718	α = 90
b = 72.275	β = 90
c = 86.819	γ = 90

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
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-23 
Deposition Author(s): Osipiuk, J., Maltseva, N., Peterson, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description