8JS5 | pdb_00008js5

Dimeric PAS domains of oxygen sensor FixL with ferric unliganded heme

PDB DOI: https://doi.org/10.2210/pdb8JS5/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: 2.95 Å
R-Value Free:
0.246 (Depositor), 0.247 (DCC)
R-Value Work:
0.207 (Depositor), 0.208 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

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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: 314.1 kDa
Atom Count: 20,358
Modeled Residue Count: 2,500
Deposited Residue Count: 2,730
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23222
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.246 (Depositor), 0.247 (DCC)
R-Value Work: 0.207 (Depositor), 0.208 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.443	α = 90
b = 194.147	β = 90
c = 269.857	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-06-26
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.