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)

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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) 

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 
• DOI: https://doi.org/10.1002/prot.10297
• Primary Citation of Related Structures:  
  1J8B

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Organizational Affiliation: 
• Center for Advanced Research In Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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