6JSD | pdb_00006jsd

Crystal structure of the domain-swapped dimer H434A variant of the C-terminal domain of HtaA from Corynebacterium glutamicum

• PDB DOI: https://doi.org/10.2210/pdb6JSD/pdb

• Classification: HEME-BINDING PROTEIN
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-04-08 Released: 2019-11-20 
• Deposition Author(s): Muraki, N., Aono, S.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.246 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the heme transfer reaction in heme uptake machinery from Corynebacteria.

Muraki, N., Kitatsuji, C., Okamoto, Y., Uchida, T., Ishimori, K., Aono, S.

(2019) Chem Commun (Camb) 55: 13864-13867

• PubMed: 31670736 
• DOI: https://doi.org/10.1039/c9cc07369h
• Primary Citation Related Structures: 
  6JS9, 6JSA, 6JSB, 6JSC, 6JSD


• PubMed Abstract: 
  

  The crystal structures of the conserved region domains of HtaA and HtaB, which act as heme binding/transport proteins in the heme uptake machinery in Corynebacterium glutamicum, are determined for the first time. The molecular mechanism of heme transfer among these proteins is proposed based on the spectroscopic and structural analyses.

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Organizational Affiliation: 
• Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.38 kDa 
• Atom Count: 2,369 
• Modeled Residue Count: 327 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical membrane protein	A, B	175	Corynebacterium glutamicum ATCC 13032	Mutation(s): 1  Gene Names: Cgl0388
UniProt
Find proteins for Q8NTB9 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NTB9  Go to UniProtKB:  Q8NTB9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	C [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.246 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.9	α = 90
b = 40.23	β = 113.97
c = 87.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Muraki, N., Aono, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	17K15081

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description