3ZJ5 | pdb_00003zj5

NEUROSPORA CRASSA CATALASE-3 EXPRESSED IN E. COLI, ORTHORHOMBIC FORM.

PDB DOI: https://doi.org/10.2210/pdb3ZJ5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Neurospora crassa
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-01-17 Released: 2013-07-10
Deposition Author(s): Zarate-Romero, A., Rudino-Pinera, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.197 (Depositor), 0.198 (DCC)
R-Value Work:
0.157 (Depositor), 0.158 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Conformational Stability and Crystal Packing: Polymorphism in Neurospora Crassa Cat-3

Zarate-Romero, A., Stojanoff, V., Rojas-Trejo, S.P., Hansberg, W., Rudino-Pinera, E.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 753

PubMed: 23832201 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309113013468
Primary Citation Related Structures:
3ZJ4, 3ZJ5, 4BIM

PubMed Abstract:
Polymorphism is frequently observed from different crystallization conditions. In proteins, the effect on conformational variability is poorly documented, with only a few reported examples. Here, three polymorphic crystal structures determined for a large-subunit catalase, CAT-3 from Neurospora crassa, are reported. Two of them belonged to new space groups, P1 and P43212, and a third structure belonged to the same space group, P212121, as the previously deposited 2.3 Å resolution structure (PDB entry 3ej6), but had a higher resolution (1.95 Å). Comparisons between these polymorphic structures highlight the conformational stability of tetrameric CAT-3 and reveal a distortion in the tetrameric structure that has not previously been described.

Organizational Affiliation

Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Chamilpa, 62210 Cuernavaca, MOR, Mexico. anzaro@ibt.unam.mx

Macromolecule Content

Total Structure Weight: 336.24 kDa
Atom Count: 24,049
Modeled Residue Count: 2,714
Deposited Residue Count: 2,984
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALASE-3	A, B, C, D	746	Neurospora crassa	Mutation(s): 0 EC: 1.11.1.6
UniProt
Find proteins for Q9C169 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q9C169 Go to UniProtKB: Q9C169
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9C169
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain BA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain BA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B] mmCIF format, chain BA [auth C]	BA [auth C], IA [auth D], J [auth A], T [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain T [auth B] Interactions & Density Focus chain BA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain T [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] FA [auth D] G [auth A] GA [auth D] H [auth A] AA [auth C], FA [auth D], G [auth A], GA [auth D], H [auth A], P [auth B], Q [auth B], R [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
AE3 Query on AE3 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain I [auth A] SDF format, chain HA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D]	HA [auth D], I [auth A], S [auth B]	2-(2-ETHOXYETHOXY)ETHANOL C₆ H₁₄ O₃ XXJWXESWEXIICW-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain I [auth A] Focus chain S [auth B] Interactions & Density Focus chain HA [auth D] Focus chain I [auth A] Focus chain S [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain V [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C]	CA [auth D] DA [auth D] E [auth A] EA [auth D] F [auth A] CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.197 (Depositor), 0.198 (DCC)
R-Value Work: 0.157 (Depositor), 0.158 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.52	α = 90
b = 154.8	β = 90
c = 160.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-10

Deposition Author(s):

Zarate-Romero, A.

Rudino-Pinera, E.

Revision History (Full details and data files)

Version 1.0: 2013-07-10
Type: Initial release
Version 1.1: 2013-07-17
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description