4P5B | pdb_00004p5b

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

PDB DOI: https://doi.org/10.2210/pdb4P5B/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.216 (Depositor), 0.212 (DCC)
R-Value Work:
0.164 (Depositor), 0.163 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4P5B

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.

Macromolecule Content

Total Structure Weight: 113.29 kDa
Atom Count: 8,125
Modeled Residue Count: 933
Deposited Residue Count: 956
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C1IC19
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D]	E [auth A], I [auth B], J [auth C], M [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D]
BRU Query on BRU Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	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		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.216 (Depositor), 0.212 (DCC)
R-Value Work: 0.164 (Depositor), 0.163 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.788	α = 90
b = 59.502	β = 120.31
c = 118.981	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-12-09

Deposition Author(s):

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.