4P7C | pdb_00004p7c

Crystal structure of putative methyltransferase from Pseudomonas syringae pv. tomato

• PDB DOI: https://doi.org/10.2210/pdb4P7C/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas syringae pv. tomato str. DC3000
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-26 Released: 2014-04-09 
• Deposition Author(s): Chang, C., Mack, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Crystal structure of putative methyltransferase from Pseudomonas syringae pv. tomato

Chang, C., Mack, J., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.22 kDa 
• Atom Count: 5,785 
• Modeled Residue Count: 641 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (mo5U34)-methyltransferase	A, B	322	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0  Gene Names: cmoB, PSPTO_4213 EC: 2.1.1 (PDB Primary Data), 2.5.1 (UniProt)
UniProt
Find proteins for Q87XG5 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q87XG5  Go to UniProtKB:  Q87XG5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	C [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
ACT	D [auth A], E [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.85 Å
• R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.076	α = 90
b = 88.732	β = 90
c = 128.094	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Chang, C., Mack, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2014-04-16
  Changes: Structure summary
• Version 1.2: 2014-08-06
  Changes: Derived calculations
• Version 1.3: 2023-12-27
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.4: 2024-11-20
  Changes: Structure summary