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- PDB-1gwf: Compound II structure of Micrococcus Lysodeikticus catalase -

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Basic information

Entry
Database: PDB / ID: 1gwf
TitleCompound II structure of Micrococcus Lysodeikticus catalase
ComponentsCatalase
KeywordsOXIDOREDUCTASE / CATALASE / HYDROGEN PEROXIDE OXIDOREDUCTASE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Catalase
Similarity search - Component
Biological speciesMicrococcus luteus (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.96 Å
AuthorsMurshudov, G.N. / Grebenko, A.I. / Brannigan, J.A. / Antson, A.A. / Barynin, V.V. / Dodson, G.G. / Dauter, Z. / Wilson, K.S. / Melik-Adamyan, W.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The Structures of Micrococcus Lysodeikticus Catalase, its Ferryl Intermediate (Compound II) and Nadph Complex.
Authors: Murshudov, G.N. / Grebenko, A.I. / Brannigan, J.A. / Antson, A.A. / Barynin, V.V. / Dodson, G.G. / Dauter, Z. / Wilson, K.S. / Melik-Adamyan, W.R.
History
DepositionMar 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.page_last / _entity.pdbx_description ..._citation.page_last / _entity.pdbx_description / _entity.src_method / _pdbx_struct_mod_residue.details / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0818
Polymers57,0431
Non-polymers1,0397
Water11,223623
1
A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,32532
Polymers228,1704
Non-polymers4,15528
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)106.190, 106.190, 105.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2062-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catalase


Mass: 57042.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrococcus luteus (bacteria) / Gene: katA / Production host: Escherichia coli (E. coli) / References: UniProt: P29422, catalase

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Non-polymers , 5 types, 630 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growpH: 5.2 / Details: pH 5.20

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.936→74.536 Å / Num. obs: 41376 / % possible obs: 99.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.96→74.54 Å / SU B: 2.755 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R Free: 0.128 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.18966 2189 5 %RANDOM
Rwork0.14095 ---
obs0.08935 41376 99.15 %-
Refinement stepCycle: LAST / Resolution: 1.96→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 67 623 4676

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