1FX3

CRYSTAL STRUCTURE OF H. INFLUENZAE SECB

• PDB DOI: https://doi.org/10.2210/pdb1FX3/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-09-25 Released: 2000-12-06 
• Deposition Author(s): Xu, Z., Knafels, J.D., Yoshino, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.301 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Crystal structure of the bacterial protein export chaperone secB.

Xu, Z., Knafels, J.D., Yoshino, K.

(2000) Nat Struct Biol 7: 1172-1177

• PubMed: 11101901 
• DOI: https://doi.org/10.1038/82040
• Primary Citation of Related Structures:  
  1FX3


• PubMed Abstract: 
  

  SecB is a bacterial molecular chaperone involved in mediating translocation of newly synthesized polypeptides across the cytoplasmic membrane of bacteria. The crystal structure of SecB from Haemophilus influenzae shows that the molecule is a tetramer organized as a dimer of dimers. Two long channels run along the side of the molecule. These are bounded by flexible loops and lined with conserved hydrophobic amino acids, which define a suitable environment for binding non-native polypeptides. The structure also reveals an acidic region on the top surface of the molecule, several residues of which have been implicated in binding to SecA, its downstream target.

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Organizational Affiliation: 

Department of Biological Chemistry, The University of Michigan Medical School, 1301 E. Catherine Road, Ann Arbor, Michigan 48109, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.59 kDa 
• Atom Count: 4,485 
• Modelled Residue Count: 569 
• Deposited Residue Count: 676 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN-EXPORT PROTEIN SECB	A, B, C, D	169	Haemophilus influenzae	Mutation(s): 0
UniProt
Find proteins for P44853 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44853  Go to UniProtKB:  P44853

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.301 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.344	α = 90
b = 126.344	β = 90
c = 148.333	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-06 
Deposition Author(s): Xu, Z., Knafels, J.D., Yoshino, K.

Revision History  

• Version 1.0: 2000-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references