7EMP | pdb_00007emp

Crystal Structure of HasAp Capturing Chromium Tetraphenylporphyrin

PDB DOI: https://doi.org/10.2210/pdb7EMP/pdb

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

Deposited: 2021-04-14 Released: 2022-04-20
Deposition Author(s): Shisaka, Y., Sakakibara, E., Sugimoto, H., Shoji, O.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.165 (Depositor), 0.166 (DCC)
R-Value Work:
0.125 (Depositor), 0.126 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Tetraphenylporphyrin Enters the Ring: First Example of a Complex between Highly Bulky Porphyrins and a Protein.

Shisaka, Y., Sakakibara, E., Suzuki, K., Stanfield, J.K., Onoda, H., Ueda, G., Hatano, M., Sugimoto, H., Shoji, O.

(2022) Chembiochem 23: e202200095-e202200095

PubMed: 35352458 Search on PubMed
DOI: https://doi.org/10.1002/cbic.202200095
Primary Citation Related Structures:
7EMO, 7EMP, 7EMQ, 7EMR, 7EMS, 7EMT, 7EMU, 7EMV, 7EMW, 7VM1

PubMed Abstract:
Tetraphenylporphyrin (TPP) is a symmetrically substituted synthetic porphyrin whose properties can be readily modified, providing it with significant advantages over naturally occurring porphyrins. Herein, we report the first example of a stable complex between a native biomolecule, the haemoprotein HasA, and TPP as well as its derivatives. The X-ray crystal structures of nine different HasA-TPP complexes were solved at high resolutions. HasA capturing TPP derivatives was also demonstrated to inhibit growth of the opportunistic pathogen Pseudomonas aeruginosa. Mutant variants of HasA binding FeTPP were shown to possess a different mode of coordination, permitting the cyclopropanation of styrene.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.

Macromolecule Content

Total Structure Weight: 60.69 kDa
Atom Count: 4,809
Modeled Residue Count: 549
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G3XD33
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J7U (Subject of Investigation/LOI) Query on J7U Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C]	D [auth A], I [auth B], N [auth C]	chromium-5,10,15,20-tetraphenylporphyrin C₄₄ H₂₈ Cr N₄ NOFMEAOHIQIURG-DAJBKUBHSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C]
CXS Query on CXS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C]	F [auth A], J [auth B], K [auth B], L [auth B], P [auth C]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C]
NHE Query on NHE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain O [auth C]	E [auth A], O [auth C]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain O [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain R [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain R [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain R [auth C]	G [auth A], H [auth A], R [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C]	M [auth B], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain M [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.165 (Depositor), 0.166 (DCC)
R-Value Work: 0.125 (Depositor), 0.126 (DCC)
R-Value Observed: 0.127 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.956	α = 90
b = 84.956	β = 90
c = 84.452	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H02084
Japan Science and Technology	Japan	JPMJCR15P3
Japan Society for the Promotion of Science (JSPS)	Japan	JP18J15250