1J8B | pdb_00001j8b

Structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function

PDB DOI: https://doi.org/10.2210/pdb1J8B/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Haemophilus influenzae Rd KW20
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2001-05-21 Released: 2003-01-14
Deposition Author(s): Lim, K., Tempcyzk, A., Toedt, J., Parsons, J.F., Howard, A., Eisenstein, E., Herzberg, O., Structure 2 Function Project (S2F)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.263 (Depositor), 0.264 (DCC)
R-Value Work:
0.180 (Depositor), 0.195 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 1J8B

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

Literature

Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR

Lim, K., Tempcyzk, A., Parsons, J.F., Bonander, N., Toedt, J., Kelman, Z., Howard, A., Eisenstein, E., Herzberg, O.

(2003) Proteins 50: 375-379

PubMed: 12486730 Search on PubMed
DOI: https://doi.org/10.1002/prot.10297
Primary Citation Related Structures:
1J8B

Organizational Affiliation

Center for Advanced Research In Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

Macromolecule Content

Total Structure Weight: 12.73 kDa
Atom Count: 904
Modeled Residue Count: 92
Deposited Residue Count: 112
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YbaB	A	112	Haemophilus influenzae Rd KW20	Mutation(s): 10 Gene Names: HI0442
UniProt
Find proteins for P44711 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44711 Go to UniProtKB: P44711
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P44711
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: 1.75 Å
R-Value Free: 0.263 (Depositor), 0.264 (DCC)
R-Value Work: 0.180 (Depositor), 0.195 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.39	α = 90
b = 132.79	β = 90
c = 36.22	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
SHELX	model building
MLPHARE	phasing
DM	model building
CNS	refinement
SHELX	phasing
DM	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-01-14

Deposition Author(s):

Structure 2 Function Project (S2F)

Revision History (Full details and data files)

Version 1.0: 2003-01-14
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2012-09-26
Changes: Database references
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.