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- PDB-5yem: CATPO mutant - T188F -

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Basic information

Entry
Database: PDB / ID: 5yem
TitleCATPO mutant - T188F
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
Catalase, four-helical 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 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Catalase, four-helical 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 / Hemocyanin, N-terminal domain / 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 / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesMycothermus thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsYuzugullu Karakus, Y. / Balci, S. / Goc, G. / Pearson, A.R. / Yorke, B.
Funding support Turkey, 1items
OrganizationGrant numberCountry
TUBITAK113Z744 Turkey
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, Y.K. / Goc, G. / Zengin, M.K. / Balci, S.U. / Yorke, B.A. / Pearson, A.R.
History
DepositionSep 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Feb 14, 2024Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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

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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)302,07518
Polymers299,2084
Non-polymers2,86714
Water40,7862264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54460 Å2
ΔGint-424 kcal/mol
Surface area72930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.109, 121.539, 186.025
Angle α, β, γ (deg.)90.000, 101.820, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Catalase


Mass: 74802.102 Da / Num. of mol.: 4 / Fragment: UNP residues 40-717 / Mutation: T188F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycothermus thermophilus (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: M4GGR5, 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2264 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97241 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97241 Å / Relative weight: 1
ReflectionResolution: 1.49→112.89 Å / Num. obs: 440118 / % possible obs: 99.3 % / Redundancy: 3.4 % / Net I/σ(I): 7.4
Reflection shellResolution: 1.49→1.51 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 1.4 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AUM

4aum


Resolution: 1.49→112.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.657 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 21980 5 %RANDOM
Rwork0.1582 ---
obs0.1596 418133 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.94 Å2 / Biso mean: 13.507 Å2 / Biso min: 1.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.49→112.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21133 0 182 2264 23579
Biso mean--9.87 19.62 -
Num. residues----2712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01923627
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220850
X-RAY DIFFRACTIONr_angle_refined_deg2.0161.94332345
X-RAY DIFFRACTIONr_angle_other_deg1.123348385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70653050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86723.8661190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18153663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.43715181
X-RAY DIFFRACTIONr_chiral_restr0.1350.23382
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02127868
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025273
LS refinement shellResolution: 1.489→1.527 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 1528 -
Rwork0.321 29896 -
all-31424 -
obs--96.1 %

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