7TMU | pdb_00007tmu

Crystal Structure of the Protein of Unknown Function YPO0625 from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb7TMU/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-20 Released: 2022-02-02
Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.234 (Depositor), 0.233 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7TMU

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

Literature

Crystal Structure of the Protein of Unknown Function YPO0625 from Yersinia pestis

Kim, Y., Chhor, G., Endres, M., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 69.43 kDa
Atom Count: 4,713
Modeled Residue Count: 579
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SRPBCC family protein	A, B, C, D	150	Yersinia pestis CO92	Mutation(s): 0 Gene Names: y3553, YP_2942, EGX46_19825
UniProt
Find proteins for A0A5P8YK04 (Yersinia pestis) Explore A0A5P8YK04 Go to UniProtKB: A0A5P8YK04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5P8YK04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], N [auth C], S [auth D], T [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain T [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain H [auth B] MOL2 format, chain R [auth D] MOL2 format, chain H [auth B] mmCIF format, chain R [auth D] mmCIF format, chain H [auth B]	H [auth B], R [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain R [auth D] Interactions & Density Focus chain H [auth B] Focus chain R [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain U [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain U [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], O [auth C], U [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A] K [auth B] L [auth B] P [auth C] Q [auth C] G [auth A], K [auth B], L [auth B], P [auth C], Q [auth C], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.234 (Depositor), 0.233 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.872	α = 90
b = 92.935	β = 92.053
c = 82.991	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
SHELXDE	phasing
Coot	model building

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-02-02
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, 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.