7AZQ | pdb_00007azq

Crystal structure of the iron/manganese cambialistic superoxide dismutase from Rhodobacter capsulatus complex with Fe

PDB DOI: https://doi.org/10.2210/pdb7AZQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodobacter capsulatus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-11-17 Released: 2021-12-01
Deposition Author(s): Ponce-Salvatierra, A., Hermoso, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.188 (Depositor), 0.195 (DCC)
R-Value Work:
0.169 (Depositor), 0.180 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7AZQ

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

Literature

Structural and functional characterization of the cambialistic superoxide dismutase from Rhodobacter capsulatus.

Ponce-Salvatierra, A., Di Capua, C., Gonzalez, J., Cortez, N., Hermoso, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 44.19 kDa
Atom Count: 3,317
Modeled Residue Count: 398
Deposited Residue Count: 398
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Fe]	A, B [auth E]	199	Rhodobacter capsulatus	Mutation(s): 0 Gene Names: sodB, sod EC: 1.15.1.1
UniProt
Find proteins for O30970 (Rhodobacter capsulatus) Explore O30970 Go to UniProtKB: O30970
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O30970
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain D [auth E] SDF format, chain C [auth A] MOL2 format, chain D [auth E] MOL2 format, chain C [auth A] mmCIF format, chain D [auth E] mmCIF format, chain C [auth A]	C [auth A], D [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth E] Interactions & Density Focus chain C [auth A] Focus chain D [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E MOL2 format, chain E mmCIF format, chain E	E	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E Interactions & Density Focus chain E

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.188 (Depositor), 0.195 (DCC)
R-Value Work: 0.169 (Depositor), 0.180 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.79	α = 90
b = 162.79	β = 90
c = 43.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Ponce-Salvatierra, A.

Revision History (Full details and data files)

Version 1.0: 2021-12-01
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.