3OA8 | pdb_00003oa8

Diheme SoxAX

PDB DOI: https://doi.org/10.2210/pdb3OA8/pdb

Classification: Heme-binding protein/Heme-binding protein
Organism(s): Ancylobacter novellus
Expression System: Rhodobacter capsulatus
Mutation(s): No

Deposited: 2010-08-04 Released: 2011-05-18
Deposition Author(s): Maher, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.230 (Depositor)
R-Value Work:
0.183 (Depositor), 0.186 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Diheme SoxAX proteins - insights into structure and function of the active site

Kilmartin, J., Maher, M.J., Krusong, K., Hanson, G.R., Bernhardt, P.V., Riley, M., Kappler, U.

To be published.

Macromolecule Content

Total Structure Weight: 163.12 kDa
Atom Count: 10,596
Modeled Residue Count: 1,227
Deposited Residue Count: 1,449
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SoxA	A, C, E	275	Ancylobacter novellus	Mutation(s): 0 EC: 2.8.5.2
UniProt
Find proteins for D7A6E5 (Ancylobacter novellus (strain ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM 12100 / NBRC 12443 / NCIMB 10456)) Explore D7A6E5 Go to UniProtKB: D7A6E5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D7A6E5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SoxX	B, D, F	208	Ancylobacter novellus	Mutation(s): 0
UniProt
Find proteins for Q7BQR5 (Ancylobacter novellus) Explore Q7BQR5 Go to UniProtKB: Q7BQR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7BQR5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain M [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain M [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E] mmCIF format, chain M [auth F]	G [auth A] H [auth B] J [auth C] K [auth D] L [auth E] G [auth A], H [auth B], J [auth C], K [auth D], L [auth E], M [auth F]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A, C, E	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.230 (Depositor)
R-Value Work: 0.183 (Depositor), 0.186 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.172	α = 110.02
b = 74.629	β = 108.08
c = 74.295	γ = 108.54

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-05-18

Deposition Author(s):

Maher, M.J.

Revision History (Full details and data files)

Version 1.0: 2011-05-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary