4KDR | pdb_00004kdr

Crystal Structure of UBIG/SAH complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Crystal Structure of the UBIG/SAH complex

Zhu, Y., Teng, M., Li, X.

To be published.

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

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-demethylubiquinone-9 3-methyltransferase223Escherichia coli K-12Mutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17993
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH

Query on SAH


Download:Ideal Coordinates CCD File
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), 0.234 (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 = 141.133α = 90
b = 39.5β = 94.4
c = 40.422γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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