8GM3

Vibrio harveyi Holo HphA

PDB DOI: https://doi.org/10.2210/pdb8GM3/pdb

Classification: METAL TRANSPORT
Organism(s): Vibrio harveyi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-03-24 Released: 2024-03-27
Deposition Author(s): Pan, C., Shah, M., Moraes, T.F.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.255
R-Value Work: 0.210
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Heme Acquisition by Slam-dependent Hemophores in Gram-negative Bacteria

Shin, H.E., Moraes, T.F.

To be published.

Macromolecule Content

Total Structure Weight: 50.64 kDa
Atom Count: 3,665
Modelled Residue Count: 436
Deposited Residue Count: 468
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemophilin	A, B	234	Vibrio harveyi	Mutation(s): 0 Gene Names: AL538_19455
UniProt
Find proteins for A0A3A1PTD6 (Vibrio harveyi) Explore A0A3A1PTD6 Go to UniProtKB: A0A3A1PTD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3A1PTD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEB (Subject of Investigation/LOI) Query on HEB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	HEME B/C C₃₄ H₃₄ Fe N₄ O₄ NEGHHAJBRZGUAY-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.255
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.438	α = 90
b = 81.08	β = 90
c = 135.577	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-115182

Revision History (Full details and data files)

Version 1.0: 2024-03-27
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.