5FD5 | pdb_00005fd5

manganese uptake regulator

PDB DOI: https://doi.org/10.2210/pdb5FD5/pdb

Classification: TRANSCRIPTION
Organism(s): Rhizobium leguminosarum bv. viciae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-12-15 Released: 2016-12-28
Deposition Author(s): Bellini, D., Lebedev, A., Keegan, R., Walsh, M.A.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.247 (Depositor), 0.246 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5FD5

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

Literature

Structure of an apo metal-free manganese uptake regulator, mur

Bellini, D., Lebedev, A., Keegan, R., Todd, J., Hemmings, A.M., Johnston, A.W., Walsh, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 83.67 kDa
Atom Count: 6,081
Modeled Residue Count: 673
Deposited Residue Count: 705
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferric uptake regulation protein	A, B, C, D, E	141	Rhizobium leguminosarum bv. viciae	Mutation(s): 1 Gene Names: fur
UniProt
Find proteins for O07315 (Rhizobium leguminosarum bv. viciae) Explore O07315 Go to UniProtKB: O07315
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O07315
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 F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain L [auth E] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain L [auth E] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain L [auth E]	F [auth B] G [auth B] H [auth C] I [auth C] J [auth D] F [auth B], G [auth B], H [auth C], I [auth C], J [auth D], L [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth E] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain M [auth E] SDF format, chain N [auth E] MOL2 format, chain K [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] mmCIF format, chain K [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E]	K [auth D], M [auth E], N [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth E] Interactions & Density Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.247 (Depositor), 0.246 (DCC)
R-Value Work: 0.222 (Depositor), 0.222 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.8	α = 90
b = 171.32	β = 90
c = 90.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT093314/Z10/Z

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations

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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.