3KM2

As-isolated TOMATO CHLOROPLAST SUPEROXIDE DISMUTASE

PDB DOI: https://doi.org/10.2210/pdb3KM2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Solanum lycopersicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-09 Released: 2010-12-01
Deposition Author(s): Galaleldeen, A., Taylor, A.B., Hart, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.252
R-Value Work: 0.220
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

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

Literature

Biophysical properties of tomato chloroplast sod

Galaleldeen, A., Taylor, A.B., Hart, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 377.03 kDa
Atom Count: 26,160
Modelled Residue Count: 3,672
Deposited Residue Count: 3,696
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn], chloroplastic	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	154	Solanum lycopersicum	Mutation(s): 0 Gene Names: SODCP.2 EC: 1.15.1.1
UniProt
Find proteins for P14831 (Solanum lycopersicum) Explore P14831 Go to UniProtKB: P14831
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14831
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth J] SDF format, chain IA [auth K] SDF format, chain JA [auth L] SDF format, chain KA [auth M] SDF format, chain LA [auth N] SDF format, chain MA [auth O] SDF format, chain NA [auth P] SDF format, chain OA [auth Q] SDF format, chain PA [auth R] SDF format, chain QA [auth S] SDF format, chain RA [auth T] SDF format, chain SA [auth U] SDF format, chain TA [auth V] SDF format, chain UA [auth W] SDF format, chain VA [auth X] SDF format, chain Y [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain JA [auth L] MOL2 format, chain KA [auth M] MOL2 format, chain LA [auth N] MOL2 format, chain MA [auth O] MOL2 format, chain NA [auth P] MOL2 format, chain OA [auth Q] MOL2 format, chain PA [auth R] MOL2 format, chain QA [auth S] MOL2 format, chain RA [auth T] MOL2 format, chain SA [auth U] MOL2 format, chain TA [auth V] MOL2 format, chain UA [auth W] MOL2 format, chain VA [auth X] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B]	AA [auth C] BA [auth D] CA [auth E] DA [auth F] EA [auth G] AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth J], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], Y [auth A], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.252
R-Value Work: 0.220
R-Value Observed: 0.222
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.033	α = 90
b = 144.523	β = 90
c = 192.178	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Galaleldeen, A.

Taylor, A.B.

Hart, P.J.

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description