6DQY | pdb_00006dqy

Crystal Structure analysis of Superoxide Dismutase from Trichoderma reesei

PDB DOI: https://doi.org/10.2210/pdb6DQY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trichoderma reesei QM6a
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-06-11 Released: 2018-12-12
Deposition Author(s): Mendoza, E.R., Stelmastchuk, L.B.F., Ferreira Junior, J.R.S., Garratt, R.C.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.207 (Depositor), 0.210 (DCC)
R-Value Work:
0.162 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Superoxide Dismutase from Trichoderma reesei

Mendoza, E.R., Stelmastchuk, L.B.F., Ferreira Junior, J.R.S., Garratt, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 559.57 kDa
Atom Count: 41,443
Modeled Residue Count: 4,983
Deposited Residue Count: 5,088
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	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	212	Trichoderma reesei QM6a	Mutation(s): 0 Gene Names: TRIREDRAFT_66345 EC: 1.15.1.1
UniProt
Find proteins for G0RQS7 (Hypocrea jecorina (strain QM6a)) Explore G0RQS7 Go to UniProtKB: G0RQS7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0RQS7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth A] SDF format, chain VA [auth X] SDF format, chain UA [auth W] SDF format, chain TA [auth V] SDF format, chain SA [auth U] SDF format, chain RA [auth T] SDF format, chain QA [auth S] SDF format, chain PA [auth R] SDF format, chain OA [auth Q] SDF format, chain NA [auth P] SDF format, chain MA [auth O] SDF format, chain LA [auth N] SDF format, chain KA [auth M] SDF format, chain JA [auth L] SDF format, chain IA [auth K] SDF format, chain HA [auth J] SDF format, chain GA [auth I] SDF format, chain FA [auth H] SDF format, chain EA [auth G] SDF format, chain DA [auth F] SDF format, chain CA [auth E] SDF format, chain BA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain VA [auth X] MOL2 format, chain UA [auth W] MOL2 format, chain TA [auth V] MOL2 format, chain SA [auth U] MOL2 format, chain RA [auth T] MOL2 format, chain QA [auth S] MOL2 format, chain PA [auth R] MOL2 format, chain OA [auth Q] MOL2 format, chain NA [auth P] MOL2 format, chain MA [auth O] MOL2 format, chain LA [auth N] MOL2 format, chain KA [auth M] MOL2 format, chain JA [auth L] MOL2 format, chain IA [auth K] MOL2 format, chain HA [auth J] MOL2 format, chain GA [auth I] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain VA [auth X] mmCIF format, chain UA [auth W] mmCIF format, chain TA [auth V] mmCIF format, chain SA [auth U] mmCIF format, chain RA [auth T] mmCIF format, chain QA [auth S] mmCIF format, chain PA [auth R] mmCIF format, chain OA [auth Q] mmCIF format, chain NA [auth P] mmCIF format, chain MA [auth O] mmCIF format, chain LA [auth N] mmCIF format, chain KA [auth M] mmCIF format, chain JA [auth L] mmCIF format, chain IA [auth K] mmCIF format, chain HA [auth J] mmCIF format, chain GA [auth I] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth C]	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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-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: 2.30 Å
R-Value Free: 0.207 (Depositor), 0.210 (DCC)
R-Value Work: 0.162 (Depositor), 0.160 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.77	α = 91.59
b = 113.06	β = 93.79
c = 162.71	γ = 89.98

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

Mendoza, E.R.

Stelmastchuk, L.B.F.

Ferreira Junior, J.R.S.

Garratt, R.C.

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/01855-2

Revision History (Full details and data files)

Version 1.0: 2018-12-12
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations, Refinement description