4J07 | pdb_00004j07

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 (Depositor), 0.250 (DCC)
R-Value Work:
0.208 (Depositor), 0.214 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 743
Deposited Residue Count: 905
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 O [auth E] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	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 P [auth E] SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	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 (Depositor), 0.250 (DCC)
R-Value Work: 0.208 (Depositor), 0.214 (DCC)
R-Value Observed: 0.210 (Depositor)

Diffraction Data:

Space Group: P 6₅ 2 2

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

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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

4J07 | pdb_00004j07

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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