4P5A

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

• PDB DOI: https://doi.org/10.2210/pdb4P5A/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces asoensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-15 Released: 2015-12-09 
• Deposition Author(s): Li, Y., Chen, W., Li, J., Xia, Z., Deng, Z., Zhou, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.193 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 113.26 kDa 
• Atom Count: 8,303 
• Modelled Residue Count: 901 
• Deposited Residue Count: 956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase ThyX	A, B, C, D	239	Streptomyces asoensis	Mutation(s): 0  Gene Names: polB, thyX EC: 2.1.1.148
UniProt
Find proteins for C1IC19 (Streptomyces asoensis) Explore C1IC19  Go to UniProtKB:  C1IC19

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], H [auth B], I [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
5BU	F [auth A], G [auth B], J [auth C], K [auth D]	5-BROMO-URIDINE-5'-MONOPHOSPHATE C9 H12 Br N2 O9 P IDPVUMJNEZFMNU-UAKXSSHOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.193 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.897	α = 90
b = 94.16	β = 98.3
c = 91.948	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Li, Y., Chen, W., Li, J., Xia, Z., Deng, Z., Zhou, J.

Revision History  

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