4YMP | pdb_00004ymp

Crystal structure of the Bacillus anthracis Hal NEAT domain in complex with heme

PDB DOI: https://doi.org/10.2210/pdb4YMP/pdb

Classification: Heme-Binding Protein
Organism(s): Bacillus anthracis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-03-07 Released: 2016-07-20
Deposition Author(s): Torres, R., Goulding, C.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free:
0.326 (Depositor), 0.347 (DCC)
R-Value Work:
0.276 (Depositor), 0.291 (DCC)
R-Value Observed:
0.281 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the Bacillus anthracis Hal NEAT domain in complex with heme

Torres, R., Goulding, C.W.

To be published.

Macromolecule Content

Total Structure Weight: 31.56 kDa
Atom Count: 1,874
Modeled Residue Count: 215
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Internalin	A, B [auth C]	130	Bacillus anthracis	Mutation(s): 0 Gene Names: HYU01_03010
UniProt
Find proteins for A0A1C7D116 (Bacillus anthracis) Explore A0A1C7D116 Go to UniProtKB: A0A1C7D116
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1C7D116
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain C [auth A] MOL2 format, chain D [auth C] MOL2 format, chain C [auth A] mmCIF format, chain D [auth C] mmCIF format, chain C [auth A]	C [auth A], D [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.326 (Depositor), 0.347 (DCC)
R-Value Work: 0.276 (Depositor), 0.291 (DCC)
R-Value Observed: 0.281 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.85	α = 90
b = 84.85	β = 90
c = 178.27	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHENIX	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations, 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.