7LRH | pdb_00007lrh

C-terminal domain of RibD from Brucella abortus (5-amino-6-ribosylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate reductase)

PDB DOI: https://doi.org/10.2210/pdb7LRH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brucella abortus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-02-16 Released: 2022-03-16
Deposition Author(s): Bonomi, H.R., Cerutti, M.L., Posadas, D.M., Goldbaum, F.A., Klinke, S.
Funding Organization(s): Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.274 (Depositor), 0.279 (DCC)
R-Value Work:
0.234 (Depositor), 0.239 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7LRH

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

Literature

C-terminal domain of RibD from Brucella abortus (5-amino-6-ribosylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate reductase)

Bonomi, H.R., Cerutti, M.L., Posadas, D.M., Goldbaum, F.A., Klinke, S.

To be published.

Macromolecule Content

Total Structure Weight: 97.96 kDa
Atom Count: 6,426
Modeled Residue Count: 850
Deposited Residue Count: 900
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin biosynthesis protein RibD	A, B, C, D	225	Brucella abortus	Mutation(s): 0 Gene Names: ribD, E4190_008840 EC: 3.5.4.26 (PDB Primary Data), 1.1.1.193 (PDB Primary Data)
UniProt
Find proteins for Q2YN93 (Brucella abortus (strain 2308)) Explore Q2YN93 Go to UniProtKB: Q2YN93
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YN93
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.274 (Depositor), 0.279 (DCC)
R-Value Work: 0.234 (Depositor), 0.239 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.91	α = 95.988
b = 56.7	β = 91.249
c = 79.6	γ = 113.164

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
BALBES	phasing
PHENIX	refinement
REFMAC	refinement
Coot	model building
ARP/wARP	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)	Argentina	PICT 2014-0959

Revision History (Full details and data files)

Version 1.0: 2022-03-16
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.