4J07

Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae

PDB DOI: https://doi.org/10.2210/pdb4J07/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium leprae Br4923
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-01-30 Released: 2013-03-06
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.246
R-Value Work: 0.208
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a Probable Riboflavin Synthase, Beta chain RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 93.91 kDa
Atom Count: 5,962
Modelled Residue Count: 743
Deposited Residue Count: 905
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A, B, C, D, E	181	Mycobacterium leprae Br4923	Mutation(s): 0 Gene Names: MLBr00560, ribH EC: 2.5.1.78
UniProt
Find proteins for B8ZUN3 (Mycobacterium leprae (strain Br4923)) Explore B8ZUN3 Go to UniProtKB: B8ZUN3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8ZUN3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E]	G [auth A] I [auth B] K [auth C] L [auth D] M [auth D] G [auth A], I [auth B], K [auth C], L [auth D], M [auth D], O [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E]	F [auth A], H [auth B], J [auth C], N [auth D], P [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain N [auth D] Focus chain P [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain N [auth D] Focus chain P [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.246
R-Value Work: 0.208
R-Value Observed: 0.210
Space Group: P 6₅ 2 2
Diffraction Data: https://doi.org/10.18430/M34J07

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.95	α = 90
b = 109.95	β = 90
c = 288.33	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

4J07

Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae

Crystal structure of a Probable Riboflavin Synthase, Beta chain RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)