5KHL | pdb_00005khl

Crystal Structure of periplasmic Heme binding protein HutB of Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb5KHL/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio cholerae O395
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-15 Released: 2017-02-22
Deposition Author(s): Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J.
Funding Organization(s): DAE (BRNS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.200 (Depositor), 0.206 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of periplasmic Heme binding protein HutB of Vibrio cholerae

Agarwal, S., Biswas, M., Dasgupta, J.

To be published.

Macromolecule Content

Total Structure Weight: 28.96 kDa
Atom Count: 1,968
Modeled Residue Count: 257
Deposited Residue Count: 271
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemin ABC transporter, periplasmic hemin-binding protein HutB	A [auth B]	271	Vibrio cholerae O395	Mutation(s): 0 Gene Names: hutB, VC0395_0324
UniProt
Find proteins for A0A0H3AE70 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AE70 Go to UniProtKB: A0A0H3AE70
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3AE70
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.256 (Depositor), 0.256 (DCC)
R-Value Work: 0.200 (Depositor), 0.206 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.884	α = 90
b = 62.884	β = 90
c = 135.774	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
SCALA	data scaling
PHASER	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Funding Organization	Location	Grant Number
DAE (BRNS)	India	2013/37B/26/brns

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.