Macromolecule Content

Total Structure Weight: 163.3 kDa
Atom Count: 11,267
Modelled Residue Count: 1,437
Deposited Residue Count: 1,492
Unique protein chains: 1

2B3Z

Crystal structure of a bifunctional deaminase and reductase involved in riboflavin biosynthesis

PDB DOI: 10.2210/pdb2B3Z/pdb

Classification: HYDROLASE, OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-09-22 Released: 2005-11-29
Deposition Author(s): Chen, S.J., Chang, Y.C., Liaw, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.277
R-Value Work: 0.226
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a bifunctional deaminase and reductase involved in riboflavin biosynthesis

Chen, S.J., Chang, Y.C., Liaw, S.H.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin biosynthesis protein ribD	A, B, C, D	373	Bacillus subtilis	Mutation(s): 0 Gene Names: ribG EC: 3.5.4.26 (PDB Primary Data), 1.1.1.193 (PDB Primary Data)
UniProt
Find proteins for P17618 (Bacillus subtilis (strain 168)) Explore P17618 Go to UniProtKB: P17618
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17618
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.277
R-Value Work: 0.226
R-Value Observed: 0.226
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.322	α = 90
b = 108.45	β = 90
c = 186.977	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-11-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-11-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description

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.