4KDR | pdb_00004kdr

Crystal Structure of UBIG/SAH complex

• PDB DOI: https://doi.org/10.2210/pdb4KDR/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-25 Released: 2014-04-30 
• Deposition Author(s): Zhu, Y., Teng, M., Li, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal Structure of the UBIG/SAH complex

Zhu, Y., Teng, M., Li, X.

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: 25.22 kDa 
• Atom Count: 1,660 
• Modeled Residue Count: 208 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-demethylubiquinone-9 3-methyltransferase	A	223	Escherichia coli K-12	Mutation(s): 0  Gene Names: ubiG, pufX, yfaB, b2232, JW2226 EC: 2.1.1.64 (PDB Primary Data), 2.1.1.222 (PDB Primary Data)
UniProt
Find proteins for P17993 (Escherichia coli (strain K12)) Explore P17993  Go to UniProtKB:  P17993

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	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:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.133	α = 90
b = 39.5	β = 94.4
c = 40.422	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Zhu, Y., Teng, M., Li, X.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations