6JOV

Crystal structure of a hypothetical Fe Superoxide dismutase

PDB DOI: https://doi.org/10.2210/pdb6JOV/pdb

Classification: METAL BINDING PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-23 Released: 2020-01-29
Deposition Author(s): Bose, S., Purushothaman, S.S., Subramanian, R.
Funding Organization(s): Department of Biotechnology (India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.227
R-Value Work: 0.181
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a hypothetical Fe Superoxide dismutase

Ashok, A., Bose, S., Jain, C., Purushothaman, S.S., Subramanian, R.

To be published.

Macromolecule Content

Total Structure Weight: 102.25 kDa
Atom Count: 6,843
Modelled Residue Count: 790
Deposited Residue Count: 876
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe-Superoxide dismutase	A, B, C, D	219	synthetic construct	Mutation(s): 0 EC: 1.15.1.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain N [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain N [auth B]	IA [auth D], N [auth B]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain IA [auth D] Focus chain N [auth B] Interactions & Density Focus chain IA [auth D] Focus chain N [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain JA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain JA [auth D]	F [auth A], JA [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain JA [auth D] Interactions & Density Focus chain F [auth A] Focus chain JA [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B]	G [auth A] H [auth A] O [auth B] P [auth B] X [auth C] G [auth A], H [auth A], O [auth B], P [auth B], X [auth C], Y [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Focus chain Y [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Z [auth C] SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain J [auth A] SDF format, chain KA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	AA [auth C] BA [auth C] CA [auth C] I [auth A] J [auth A] AA [auth C], BA [auth C], CA [auth C], I [auth A], J [auth A], KA [auth D], Q [auth B], R [auth B], S [auth B], Z [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain OA [auth D] SDF format, chain U [auth B] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain PA [auth D] SDF format, chain T [auth B] SDF format, chain V [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B]	DA [auth C] EA [auth C] FA [auth C] GA [auth C] K [auth A] DA [auth C], EA [auth C], FA [auth C], GA [auth C], K [auth A], L [auth A], LA [auth D], MA [auth D], NA [auth D], OA [auth D], PA [auth D], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain E [auth A] SDF format, chain HA [auth D] SDF format, chain W [auth C] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain W [auth C]	E [auth A], HA [auth D], M [auth B], W [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain HA [auth D] Focus chain M [auth B] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain HA [auth D] Focus chain M [auth B] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.227
R-Value Work: 0.181
R-Value Observed: 0.184
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.018	α = 82.28
b = 55.088	β = 89.61
c = 74.623	γ = 68.49

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Bose, S.

Purushothaman, S.S.

Subramanian, R.

Funding Organization	Location	Grant Number
Department of Biotechnology (India)	India	--

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description