2IJR | pdb_00002ijr

Crystal structure of a protein api92 from Yersinia pseudotuberculosis, Pfam DUF1281

PDB DOI: https://doi.org/10.2210/pdb2IJR/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Yersinia pseudotuberculosis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-09-30 Released: 2006-10-31
Deposition Author(s): Jin, X., Min, T., Bonanno, J.B., Sauder, J.M., Wasserman, S., Smith, D., Burley, S.K., Shapiro, L., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.279 (Depositor), 0.277 (DCC)
R-Value Work:
0.225 (Depositor), 0.220 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2IJR

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a hypothetical protein from Yersinia pseudotuberculosis

Jin, X., Min, T., Bonanno, J.B., Sauder, J.M., Wasserman, S., Smith, D., Burley, S.K., Shapiro, L.

To be published.

Macromolecule Content

Total Structure Weight: 34.16 kDa
Atom Count: 2,285
Modeled Residue Count: 282
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein api92	A	300	Yersinia pseudotuberculosis	Mutation(s): 8 Gene Names: api92
UniProt
Find proteins for Q6EVP2 (Yersinia pseudotuberculosis) Explore Q6EVP2 Go to UniProtKB: Q6EVP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6EVP2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.279 (Depositor), 0.277 (DCC)
R-Value Work: 0.225 (Depositor), 0.220 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.656	α = 90
b = 88.656	β = 90
c = 218.227	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-10-31

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2006-10-31
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-10-30
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.