7TE5 | pdb_00007te5

Crystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb7TE5/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-04 Released: 2022-01-12
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: 1.85 Å
R-Value Free:
0.207 (Depositor), 0.210 (DCC)
R-Value Work:
0.167 (Depositor)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7TE5

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

Literature

Crystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK 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: 64.33 kDa
Atom Count: 4,812
Modeled Residue Count: 568
Deposited Residue Count: 584
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pirin family protein Yhak	A, B	292	Yersinia pestis CO92	Mutation(s): 0 Gene Names: YP_1950, EGX46_10965
UniProt
Find proteins for A0A2U2H063 (Yersinia pestis) Explore A0A2U2H063 Go to UniProtKB: A0A2U2H063
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2U2H063
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.207 (Depositor), 0.210 (DCC)
R-Value Work: 0.167 (Depositor)
R-Value Observed: 0.175 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.442	α = 90
b = 66.442	β = 90
c = 122.546	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data scaling
HKL-3000	data processing
HKL-3000	phasing
MLPHARE	phasing
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-12

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: 2022-01-12
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary

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.