6JLG | pdb_00006jlg

Crystal Structure of HasAp with Co-9,10,19,20-Tetraphenylporphycene

PDB DOI: https://doi.org/10.2210/pdb6JLG/pdb

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

Deposited: 2019-03-05 Released: 2020-03-11
Deposition Author(s): Sakakibara, E., Shisaka, Y., Onoda, H., Sugimoto, H., Shiro, Y., Watanabe, Y., Shoji, O.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.241 (Depositor), 0.245 (DCC)
R-Value Work:
0.213 (Depositor), 0.217 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Highly malleable haem-binding site of the haemoprotein HasA permits stable accommodation of bulky tetraphenylporphycenes.

Sakakibara, E., Shisaka, Y., Onoda, H., Koga, D., Xu, N., Ono, T., Hisaeda, Y., Sugimoto, H., Shiro, Y., Watanabe, Y., Shoji, O.

(2019) RSC Adv 9: 18697-18702

DOI: https://doi.org/10.1039/C9RA02872B

Macromolecule Content

Total Structure Weight: 157.6 kDa
Atom Count: 11,178
Modeled Residue Count: 1,444
Deposited Residue Count: 1,472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme acquisition protein HasA	A, B, C, D, E A, B, C, D, E, F, G, H	184	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: hasA, C0044_25535, C8257_08650, CAZ10_20450, CGU42_19580, DT376_18720, DZ940_32815, NCTC13719_01562, PAERUG_E15_London_28_01_14_06674, PAMH19_1664... hasA, C0044_25535, C8257_08650, CAZ10_20450, CGU42_19580, DT376_18720, DZ940_32815, NCTC13719_01562, PAERUG_E15_London_28_01_14_06674, PAMH19_1664, RW109_RW109_02394
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BWU Query on BWU Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain U [auth F] SDF format, chain V [auth G] SDF format, chain Z [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth G] mmCIF format, chain Z [auth H]	I [auth A] L [auth B] O [auth C] P [auth D] R [auth E] I [auth A], L [auth B], O [auth C], P [auth D], R [auth E], U [auth F], V [auth G], Z [auth H]	Tetraphenylporphycene contating cobalt C₄₄ H₂₈ Co N₄ PWICVPBSZDUOSZ-LIDSSYNJSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain Z [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain Z [auth H]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain W [auth G] MOL2 format, chain S [auth E] MOL2 format, chain W [auth G] mmCIF format, chain S [auth E] mmCIF format, chain W [auth G]	S [auth E], W [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain S [auth E] Focus chain W [auth G] Interactions & Density Focus chain S [auth E] Focus chain W [auth G]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain X [auth G] SDF format, chain Y [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] mmCIF format, chain AA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G]	AA [auth H] J [auth A] K [auth A] M [auth B] N [auth B] AA [auth H], J [auth A], K [auth A], M [auth B], N [auth B], Q [auth D], T [auth E], X [auth G], Y [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth D] Focus chain T [auth E] Focus chain X [auth G] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth D] Focus chain T [auth E] Focus chain X [auth G] Focus chain Y [auth G]