8JS7 | pdb_00008js7

Dimeric PAS domains of oxygen sensor FixL in complex with imidazole-bound heme

PDB DOI: https://doi.org/10.2210/pdb8JS7/pdb

Classification: TRANSFERASE
Organism(s): Bradyrhizobium diazoefficiens USDA 110
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-19 Released: 2024-06-26
Deposition Author(s): Kamaya, M., Koteishi, H., Sawai, H., Sugimoto, H., Shiro, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.248 (Depositor), 0.250 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Dimeric PAS domains of oxygen sensor FixL in complex with imidazole-bound heme.

Koteishi, H., Sugimoto, H.

To be published.

Macromolecule Content

Total Structure Weight: 314.79 kDa
Atom Count: 20,488
Modeled Residue Count: 2,506
Deposited Residue Count: 2,730
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein FixL	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	273	Bradyrhizobium diazoefficiens USDA 110	Mutation(s): 0 Gene Names: fixL, bll2760 EC: 2.7.13.3
UniProt
Find proteins for P23222 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore P23222 Go to UniProtKB: P23222
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23222
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain MA [auth I] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain RA [auth J] SDF format, chain W [auth D] SDF format, chain Y [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth J] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain MA [auth I] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain RA [auth J] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E]	DA [auth F] FA [auth G] K [auth A] KA [auth H] MA [auth I] DA [auth F], FA [auth G], K [auth A], KA [auth H], MA [auth I], P [auth B], R [auth C], RA [auth J], W [auth D], Y [auth E]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain DA [auth F] Focus chain FA [auth G] Focus chain K [auth A] Focus chain KA [auth H] Focus chain MA [auth I] Focus chain P [auth B] Focus chain R [auth C] Focus chain RA [auth J] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain DA [auth F] Focus chain FA [auth G] Focus chain K [auth A] Focus chain KA [auth H] Focus chain MA [auth I] Focus chain P [auth B] Focus chain R [auth C] Focus chain RA [auth J] Focus chain W [auth D] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain GA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain NA [auth I] SDF format, chain O [auth B] SDF format, chain OA [auth I] SDF format, chain QA [auth J] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Z [auth E] SDF format, chain V [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth I] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth I] MOL2 format, chain QA [auth J] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth I] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth I] mmCIF format, chain QA [auth J] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D]	AA [auth E] CA [auth F] GA [auth G] IA [auth H] JA [auth H] AA [auth E], CA [auth F], GA [auth G], IA [auth H], JA [auth H], L [auth A], N [auth B], NA [auth I], O [auth B], OA [auth I], QA [auth J], S [auth C], T [auth C], V [auth D], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain L [auth A] Focus chain N [auth B] Focus chain NA [auth I] Focus chain O [auth B] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain L [auth A] Focus chain N [auth B] Focus chain NA [auth I] Focus chain O [auth B] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain Z [auth E]
IMD (Subject of Investigation/LOI) Query on IMD Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain HA [auth G] SDF format, chain LA [auth H] SDF format, chain PA [auth I] SDF format, chain Q [auth B] SDF format, chain X [auth D] SDF format, chain U [auth C] SDF format, chain SA [auth J] SDF format, chain M [auth A] SDF format, chain EA [auth F] MOL2 format, chain BA [auth E] MOL2 format, chain HA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain PA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] MOL2 format, chain SA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain EA [auth F] mmCIF format, chain BA [auth E] mmCIF format, chain HA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain PA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C] mmCIF format, chain SA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain EA [auth F]	BA [auth E] EA [auth F] HA [auth G] LA [auth H] M [auth A] BA [auth E], EA [auth F], HA [auth G], LA [auth H], M [auth A], PA [auth I], Q [auth B], SA [auth J], U [auth C], X [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain LA [auth H] Focus chain M [auth A] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain SA [auth J] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain LA [auth H] Focus chain M [auth A] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain SA [auth J] Focus chain U [auth C] Focus chain X [auth D]