4P5B

Crystal structure of a UMP/dUMP methylase PolB from Streptomyces cacaoi bound with 5-Br dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a UMP/dUMP methylase PolB form Streptomyces cacaoi bound with 5-Br dUMP

Li, Y.Chen, W.Li, J.Xia, Z.Deng, Z.Zhou, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate synthase ThyX
A, B, C, D
239Streptomyces asoensisMutation(s): 0 
Gene Names: polBthyX
EC: 2.1.1.148
UniProt
Find proteins for C1IC19 (Streptomyces asoensis)
Explore C1IC19 
Go to UniProtKB:  C1IC19
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1IC19
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
J [auth C],
M [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
BRU
Query on BRU

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth C],
L [auth D]
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H12 Br N2 O8 P
LHLHVDBXXZVYJT-RRKCRQDMSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.788α = 90
b = 59.502β = 120.31
c = 118.981γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Data collection, Database references, Derived calculations