4FFK | pdb_00004ffk

X-ray structure of iron superoxide dismutase from Acidilobus saccharovorans

PDB DOI: https://doi.org/10.2210/pdb4FFK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Acidilobus saccharovorans 345-15
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-06-01 Released: 2012-06-27
Deposition Author(s): Safonova, T.N., Slutskaya, E.S., Dorovatovsky, P.V., Bezsudnova, E.Yu., Mardanov, A.V., Gumerov, V.M., Ravin, N.V., Skryabin, K.G., Popov, V.O., Polyakov, K.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4FFK

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

Literature

X-ray structure of iron superoxide dismutase from Acidilobus saccharovorans

Safonova, T.N., Slutskaya, E.S., Dorovatovsky, P.V., Bezsudnova, E.Yu., Mardanov, A.V., Gumerov, V.M., Ravin, N.V., Skryabin, K.G., Popov, V.O., Polyakov, K.M.

To be published.

Macromolecule Content

Total Structure Weight: 25.45 kDa
Atom Count: 1,840
Modeled Residue Count: 212
Deposited Residue Count: 223
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A	223	Acidilobus saccharovorans 345-15	Mutation(s): 0 Gene Names: ASAC_0498 EC: 1.15.1.1
UniProt
Find proteins for D9Q0R7 (Acidilobus saccharovorans (strain DSM 16705 / JCM 18335 / VKM B-2471 / 345-15)) Explore D9Q0R7 Go to UniProtKB: D9Q0R7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9Q0R7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.44	α = 90
b = 99.44	β = 90
c = 81.4	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-06-27

Deposition Author(s):

Slutskaya, E.S.

Dorovatovsky, P.V.

Bezsudnova, E.Yu.

Revision History (Full details and data files)

Version 1.0: 2012-06-27
Type: Initial release
Version 1.1: 2017-11-15
Changes: Database references, Refinement description, Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.