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- PDB-7wca: CATPO mutant - E484A -

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Basic information

Entry
Database: PDB / ID: 7wca
TitleCATPO mutant - E484A
ComponentsCatalase
KeywordsOXIDOREDUCTASE / catalase / phenol oxidase / lateral channel / mutant
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol
Similarity search - Function
Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical 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 / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesMycothermus thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsYuzugullu Karakus, Y. / Balci Unver, S. / Zengin Karatas, M. / Goc, G. / Pearson, A.R. / Yorke, B.
Funding support1items
OrganizationGrant numberCountry
Other government113Z744
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase.
Authors: Yuzugullu Karakus, Y. / Goc, G. / Zengin Karatas, M. / Balci Unver, S. / Yorke, B.A. / Pearson, A.R.
History
DepositionDec 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,00142
Polymers317,4164
Non-polymers8,58538
Water33,2561846
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area64750 Å2
ΔGint-445 kcal/mol
Surface area73550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.790, 120.200, 184.076
Angle α, β, γ (deg.)90.000, 101.720, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11C-1135-

HOH

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Components

#1: Protein
Catalase


Mass: 79354.016 Da / Num. of mol.: 4 / Mutation: E484A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycothermus thermophilus (fungus)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: M4GGR7, catalase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1846 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG400, Potassium chloride, Calcium chloride, Sodium cacodylate

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.78→46.43 Å / Num. obs: 250722 / % possible obs: 98.79 % / Redundancy: 3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 8
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.084 / Num. unique obs: 250722

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDS3.27data reduction
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AUM

4aum


Resolution: 1.78→46.43 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.144 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 12365 4.9 %RANDOM
Rwork0.1616 ---
obs0.1635 238356 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.74 Å2 / Biso mean: 21.029 Å2 / Biso min: 8.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20.04 Å2
2--0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.78→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21108 0 566 1846 23520
Biso mean--49.25 24.5 -
Num. residues----2711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01322343
X-RAY DIFFRACTIONr_bond_other_d0.0010.01720007
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.65930302
X-RAY DIFFRACTIONr_angle_other_deg1.3871.5846408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5152735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79422.0571254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.202153331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.17115160
X-RAY DIFFRACTIONr_chiral_restr0.0760.22791
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0225382
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024982
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 916 -
Rwork0.314 17636 -
all-18552 -
obs--98.9 %

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