5UHJ

The crystal structure of a natural product biosynthetic enzyme from Streptomyces sp. CB03234

PDB DOI: https://doi.org/10.2210/pdb5UHJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces sp. CB03234
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-01-11 Released: 2017-01-25
Deposition Author(s): Tan, K., Li, H., Endres, M., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.243
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a natural product biosynthetic enzyme from Streptomyces sp. CB03234

Tan, K., Li, H., Endres, M., Phillips Jr., G.N., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 29.39 kDa
Atom Count: 2,051
Modelled Residue Count: 245
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resisance protein/dioxygenase	A, B	129	Streptomyces sp. CB03234	Mutation(s): 0 Gene Names: tnmS1
UniProt
Find proteins for A0A125SA24 (Streptomyces sp. (strain CB03234)) Explore A0A125SA24 Go to UniProtKB: A0A125SA24
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A125SA24
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.243
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.836	α = 90
b = 33.346	β = 98.49
c = 101.781	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Phillips Jr., G.N.

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2020-09-23
Changes: Database references, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.