1I8D

CRYSTAL STRUCTURE OF RIBOFLAVIN SYNTHASE

PDB DOI: https://doi.org/10.2210/pdb1I8D/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2001-03-13 Released: 2001-09-19
Deposition Author(s): Liao, D.-I., Wawrzak, Z., Calabrese, J.C., Viitanen, P.V., Jordan, D.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.299
R-Value Work: 0.239

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of riboflavin synthase.

Liao, D.I., Wawrzak, Z., Calabrese, J.C., Viitanen, P.V., Jordan, D.B.

(2001) Structure 9: 399-408

PubMed: 11377200 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(01)00600-1
Primary Citation of Related Structures:
1I8D

PubMed Abstract:
Riboflavin synthase catalyzes the dismutation of two molecules of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine to yield riboflavin and 4-ribitylamino-5-amino-2,6-dihydroxypyrimidine. The homotrimer of 23 kDa subunits has no cofactor requirements for catalysis. The enzyme is nonexistent in humans and is an attractive target for antimicrobial agents of organisms whose pathogenicity depends on their ability to biosynthesize riboflavin.

Organizational Affiliation

DuPont Central Research and Development, Experimental Station, 19880, Wilmington, DE, USA. der-ing.liao@usa.dupont.com

Macromolecule Content

Total Structure Weight: 70.42 kDa
Atom Count: 4,807
Modelled Residue Count: 592
Deposited Residue Count: 639
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOFLAVIN SYNTHASE	A, B, C	213	Escherichia coli	Mutation(s): 0 Gene Names: BACTERIA EC: 2.5.1.9
UniProt
Find proteins for P0AFU8 (Escherichia coli (strain K12)) Explore P0AFU8 Go to UniProtKB: P0AFU8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AFU8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.299
R-Value Work: 0.239
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.083	α = 90
b = 61.705	β = 90
c = 219.781	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2001-09-19

Deposition Author(s):

Calabrese, J.C.

Revision History (Full details and data files)

Version 1.0: 2001-09-19
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references

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.