2IMH | pdb_00002imh

Crystal structure of protein SPO2555 from Silicibacter pomeroyi, Pfam DUF1028

PDB DOI: https://doi.org/10.2210/pdb2IMH/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Ruegeria pomeroyi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-10-04 Released: 2006-10-17
Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Slocombe, A., Ozyurt, S., Wasserman, S., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.207 (Depositor), 0.208 (DCC)
R-Value Work:
0.171 (Depositor)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2IMH

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of hypothetical protein from Silicibacter pomeroyi

Bonanno, J.B., Dickey, M., Bain, K.T., Slocombe, A., Ozyurt, S., Wasserman, S., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 49.37 kDa
Atom Count: 3,900
Modeled Residue Count: 443
Deposited Residue Count: 462
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein UNP Q5LQD5_SILPO	A, B	231	Ruegeria pomeroyi	Mutation(s): 5 Gene Names: SPO2555
UniProt
Find proteins for Q5LQD5 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LQD5 Go to UniProtKB: Q5LQD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LQD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.57 Å
R-Value Free: 0.207 (Depositor), 0.208 (DCC)
R-Value Work: 0.171 (Depositor)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.25	α = 90
b = 69.594	β = 90
c = 105.792	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-10-17

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2006-10-17
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-02-03
Changes: Advisory, Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-16
Changes: Advisory, Data collection, Database references, 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.