9BEO | pdb_00009beo

Tungstate binding protein (Tungbindin) from Eubacterium limosum with 7.5 tungstates bound

PDB DOI: https://doi.org/10.2210/pdb9BEO/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Eubacterium limosum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-16 Released: 2024-09-04
Deposition Author(s): Zhou, D., Rose, J.P., Chen, L., Wang, B.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.195 (Depositor), 0.195 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9BEO

This is version 1.0 of the entry. See complete history.

Literature

Tungstate binding protein (Tungbindin) from Eubacterium limosum with 7.5 tungstates bound

Zhou, D., Rose, J.P., Chen, L., Wang, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 51.33 kDa
Atom Count: 3,499
Modeled Residue Count: 421
Deposited Residue Count: 468
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdenum-pterin binding domain-containing protein	A, B, C, D, E A, B, C, D, E, F	78	Eubacterium limosum	Mutation(s): 0 Gene Names: C7955_103236, SAMN04515624_10415
UniProt
Find proteins for A0A0U3FVB3 (Eubacterium limosum) Explore A0A0U3FVB3 Go to UniProtKB: A0A0U3FVB3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0U3FVB3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WO4 (Subject of Investigation/LOI) Query on WO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F]	TUNGSTATE(VI)ION O₄ W PBYZMCDFOULPGH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.195 (Depositor), 0.195 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.752	α = 90
b = 74.752	β = 90
c = 156.577	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
AutoSol	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM 136885

Revision History (Full details and data files)

Version 1.0: 2024-09-04
Type: Initial release

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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.