1FX3 | pdb_00001fx3

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.

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)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Department of Biological Chemistry, The University of Michigan Medical School, 1301 E. Catherine Road, Ann Arbor, Michigan 48109, USA. zhaohui@umich.edu

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P44853
Sequence Annotations Expand
Reference Sequence

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2000-12-06

Deposition Author(s):

Revision History (Full details and data files)

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

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.