3NDC | pdb_00003ndc

Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus

• PDB DOI: https://doi.org/10.2210/pdb3NDC/pdb

• Classification: TRANSFERASE
• Organism(s): Rhodobacter capsulatus SB 1003
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-07 Released: 2011-06-15 
• Deposition Author(s): Seyedarabi, A., Pickersgill, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus

Seyedarabi, A., Pickersgill, R.W.

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: 56.8 kDa 
• Atom Count: 3,706 
• Modeled Residue Count: 467 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Precorrin-4 C(11)-methyltransferase	A, B	264	Rhodobacter capsulatus SB 1003	Mutation(s): 0  Gene Names: cobM EC: 2.1.1.133
UniProt
Find proteins for O68100 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)) Explore O68100  Go to UniProtKB:  O68100

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.517	α = 90
b = 84.517	β = 90
c = 144.637	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Seyedarabi, A., Pickersgill, R.W.

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description