7VF8 | pdb_00007vf8

Crystal Structure of HasAp with Co-5-octaethyloxaporphyrinium cation

PDB DOI: https://doi.org/10.2210/pdb7VF8/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.144 (Depositor), 0.144 (DCC)
R-Value Work:
0.128 (Depositor), 0.128 (DCC)
R-Value Observed:
0.129 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of HasAp with Co-5-octaethyloxaporphyrinium cation

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

To be published.

Macromolecule Content

Total Structure Weight: 39.58 kDa
Atom Count: 3,632
Modeled Residue Count: 366
Deposited Residue Count: 368
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	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7KI (Subject of Investigation/LOI) Query on 7KI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	Co-5-octaethyloxaporphyrinium cation C₃₅ H₄₃ Co N₄ O OPQNUXJQUPQEGE-SMMVCMDLSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.144 (Depositor), 0.144 (DCC)
R-Value Work: 0.128 (Depositor), 0.128 (DCC)
R-Value Observed: 0.129 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.84	α = 90
b = 153.84	β = 90
c = 37.751	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-14

Deposition Author(s):

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