7VF7 | pdb_00007vf7

Crystal Structure of HasAp with Co-octaethylporphyrin

• PDB DOI: https://doi.org/10.2210/pdb7VF7/pdb

• Classification: METAL TRANSPORT
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli M15
• Mutation(s): No 


• Deposited: 2021-09-10 Released: 2022-09-14 
• Deposition Author(s): Takiguchi, A., Sakakibara, E., Sugimoto, H., Shoji, O., Shinokubo, H.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of HasAp with Co-octaethylporphyrin

Takiguchi, A., Sakakibara, E., Sugimoto, H., Shoji, O., Shinokubo, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.68 kDa 
• Atom Count: 5,083 
• Modeled Residue Count: 549 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme acquisition protein HasAp	A, B, C	184	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: hasAp, PA3407
UniProt
Find proteins for G3XD33 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore G3XD33  Go to UniProtKB:  G3XD33

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6KI (Subject of Investigation/LOI)	D [auth A], G [auth B], H [auth C]	Co-octaethylporphyrin C36 H44 Co N4 CILRATIHXSICFS-XTPDIVBZSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.28	α = 90
b = 76.12	β = 90
c = 168.62	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Takiguchi, A., Sakakibara, E., Sugimoto, H., Shoji, O., Shinokubo, H.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP17H01190
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP19KK0138
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	17H05896
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18H02396
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP18H02084
Japan Society for the Promotion of Science (JSPS)	Japan	JP20J11437
Japan Society for the Promotion of Science (JSPS)	Japan	JP21J15614

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description