5AZ3 | pdb_00005az3

Crystal structure of heme binding protein HmuT

PDB DOI: https://doi.org/10.2210/pdb5AZ3/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-18 Released: 2015-11-18
Deposition Author(s): Muraki, N., Aono, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.181 (Depositor), 0.181 (DCC)
R-Value Work:
0.168 (Depositor), 0.169 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural Basis for Heme Recognition by HmuT Responsible for Heme Transport to the Heme Transporter in Corynebacterium glutamicum

Muraki, N., Aono, S.

(2015) Chem Lett

DOI: https://doi.org/10.1246/cl.150894

Macromolecule Content

Total Structure Weight: 36.63 kDa
Atom Count: 2,601
Modeled Residue Count: 309
Deposited Residue Count: 344
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type transporter, periplasmic component	A	344	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: Cgl0389
UniProt
Find proteins for Q8NTB8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NTB8 Go to UniProtKB: Q8NTB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NTB8
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.181 (Depositor), 0.181 (DCC)
R-Value Work: 0.168 (Depositor), 0.169 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.04	α = 90
b = 73.04	β = 90
c = 147.32	γ = 90

Software Package:

Software Name	Purpose
iMOSFLM	data processing
SCALA	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-11-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-11-18
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection, Derived calculations
Version 1.2: 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.