2V8U | pdb_00002v8u

Atomic resolution structure of Mn catalase from Thermus Thermophilus

PDB DOI: https://doi.org/10.2210/pdb2V8U/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB27
Mutation(s): No

Deposited: 2007-08-14 Released: 2007-09-25
Deposition Author(s): Barynin, V.V., Antonyuk, S.V., Vaguine, A.A., Melik-Adamyan, W.R., Popov, A.N., Lamsin, V.S., Harrison, P.M., Artymiuk, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.121 (Depositor), 0.137 (DCC)
R-Value Work:
0.106 (Depositor), 0.122 (DCC)
R-Value Observed:
0.106 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Three-Dimentional Structure of the Enzyme Dimanganese Catalase from Thermus Thermophilus at 1 Angstrom Resolution

Antonyuk, S.V., Melik-Adamyan, W.R., Popov, A.N., Lamsin, V.S., Hempstead, P.D., Harrison, P.M., Artymyuk, P.J., Barynin, V.V.

(2000) Crystallogr Rep 45: 105

Macromolecule Content

Total Structure Weight: 67.78 kDa
Atom Count: 6,092
Modeled Residue Count: 604
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANGANESE-CONTAINING PSEUDOCATALASE	A, B	302	Thermus thermophilus HB27	Mutation(s): 0 EC: 1.11.1.6
UniProt
Find proteins for Q84DB4 (Thermus thermophilus) Explore Q84DB4 Go to UniProtKB: Q84DB4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84DB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain S [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain S [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] L [auth A] M [auth A] O [auth A] AA [auth B], BA [auth B], L [auth A], M [auth A], O [auth A], P [auth A], S [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], T [auth B], U [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth B] Focus chain U [auth B]
O Query on O Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
LI Query on LI Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], N [auth A], Q [auth B], R [auth B]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.121 (Depositor), 0.137 (DCC)
R-Value Work: 0.106 (Depositor), 0.122 (DCC)
R-Value Observed: 0.106 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.3	α = 90
b = 132.3	β = 90
c = 132.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-09-25
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Advisory, Data collection
Version 1.4: 2024-05-08
Changes: Advisory, Data collection, Database references, Derived calculations, Other