8JS6 | pdb_00008js6

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

PDB DOI: https://doi.org/10.2210/pdb8JS6/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: 2.70 Å
R-Value Free:
0.247 (Depositor), 0.240 (DCC)
R-Value Work:
0.219 (Depositor), 0.210 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 314.36 kDa
Atom Count: 20,477
Modeled Residue Count: 2,512
Deposited Residue Count: 2,730
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 KA [auth H] SDF format, chain MA [auth I] SDF format, chain Y [auth E] SDF format, chain W [auth D] SDF format, chain RA [auth J] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain K [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] MOL2 format, chain RA [auth J] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain MA [auth I] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D] mmCIF format, chain RA [auth J] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A]	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 BA [auth E] SDF format, chain CA [auth F] SDF format, chain HA [auth G] SDF format, chain IA [auth G] SDF format, chain JA [auth H] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain OA [auth I] SDF format, chain PA [auth J] SDF format, chain QA [auth J] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain M [auth A] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth I] MOL2 format, chain PA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain IA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth I] mmCIF format, chain PA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain M [auth A]	AA [auth E] BA [auth E] CA [auth F] HA [auth G] IA [auth G] AA [auth E], BA [auth E], CA [auth F], HA [auth G], IA [auth G], JA [auth H], M [auth A], N [auth A], O [auth B], OA [auth I], PA [auth J], QA [auth J], T [auth C], U [auth D], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D]
CYN (Subject of Investigation/LOI) Query on CYN Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain GA [auth G] SDF format, chain L [auth A] SDF format, chain LA [auth H] SDF format, chain NA [auth I] SDF format, chain Q [auth B] SDF format, chain SA [auth J] SDF format, chain X [auth D] SDF format, chain Z [auth E] SDF format, chain S [auth C] MOL2 format, chain EA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain NA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain SA [auth J] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain S [auth C] mmCIF format, chain EA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain NA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain SA [auth J] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain S [auth C]	EA [auth F] GA [auth G] L [auth A] LA [auth H] NA [auth I] EA [auth F], GA [auth G], L [auth A], LA [auth H], NA [auth I], Q [auth B], S [auth C], SA [auth J], X [auth D], Z [auth E]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain GA [auth G] Focus chain L [auth A] Focus chain LA [auth H] Focus chain NA [auth I] Focus chain Q [auth B] Focus chain S [auth C] Focus chain SA [auth J] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth F] Focus chain GA [auth G] Focus chain L [auth A] Focus chain LA [auth H] Focus chain NA [auth I] Focus chain Q [auth B] Focus chain S [auth C] Focus chain SA [auth J] Focus chain X [auth D] Focus chain Z [auth E]