5TW9 | pdb_00005tw9

1.50 Angstrom Crystal Structure of C-terminal Fragment (residues 322-384) of Iron Uptake System Component EfeO from Yersinia pestis.

PDB DOI: https://doi.org/10.2210/pdb5TW9/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-11-11 Released: 2016-11-30
Deposition Author(s): Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.203 (Depositor), 0.209 (DCC)
R-Value Work:
0.173 (Depositor), 0.182 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5TW9

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

Literature

1.50 Angstrom Crystal Structure of C-terminal Fragment (residues 322-384) of Iron Uptake System Component EfeO from Yersinia pestis.

Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 44.37 kDa
Atom Count: 3,683
Modeled Residue Count: 376
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron uptake system component EfeO	A, B, C, D, E A, B, C, D, E, F	63	Yersinia pestis	Mutation(s): 0 Gene Names: efeO, YPO1855, y2451, YP_1538
UniProt
Find proteins for Q0WFT9 (Yersinia pestis) Explore Q0WFT9 Go to UniProtKB: Q0WFT9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0WFT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain W [auth E] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain W [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain W [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] J [auth B] K [auth B] L [auth C] G [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth D], W [auth E], Y [auth F], Z [auth F]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain V [auth D] SDF format, chain H [auth A] SDF format, chain AA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain AA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain AA [auth F]	AA [auth F], H [auth A], V [auth D], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain H [auth A] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain H [auth A] Focus chain V [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.203 (Depositor), 0.209 (DCC)
R-Value Work: 0.173 (Depositor), 0.182 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.037	α = 90
b = 64.001	β = 90
c = 173.151	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-11-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-11-30
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Structure summary

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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.