Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 60.80 kDa 
• Atom Count: 4386 
• Modelled Residue Count: 562 
• Deposited Residue Count: 565 
• Unique protein chains: 2

7W78

Heme exporter HrtBA in complex with Mg-AMPPNP

• PDB DOI: 10.2210/pdb7W78/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Corynebacterium diphtheriae NCTC 13129
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2021-12-04 Released: 2022-06-22 
• Deposition Author(s): Hisano, T., Nakamura, H., Rahman, M.M., Tosha, T., Shirouzu, M., Shiro, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 0.251 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

heme exporter complexed with AMPPNP

Nakamura, H., Hisano, T., Rahman, M.M., Tosha, T., Shirouzu, M., Shiro, Y.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ABC transport system, ATP-binding protein	A	221	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0  Gene Names: DIP2323
UniProt
Find proteins for Q6NEF2 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEF2  Go to UniProtKB:  Q6NEF2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ABC transport system integral membrane protein	B	344	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0  Gene Names: DIP2324 Membrane Entity: Yes
UniProt
Find proteins for Q6NEF1 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEF1  Go to UniProtKB:  Q6NEF1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MYZ	H [auth B], I [auth B]	Myristoleic acid C14 H26 O2 YWWVWXASSLXJHU-WAYWQWQTSA-N
D12	J [auth B]	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 0.251 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.981	α = 90
b = 168.981	β = 90
c = 94.665	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2021-12-04 
• Released Date: 2022-06-22 
Deposition Author(s): Hisano, T., Nakamura, H., Rahman, M.M., Tosha, T., Shirouzu, M., Shiro, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	26220807
Japan Society for the Promotion of Science (JSPS)	Japan	16K07309
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H00926
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05761

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release