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- PDB-5xzn: CATPO mutant - V228C -

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Basic information

Entry
Database: PDB / ID: 5xzn
TitleCATPO mutant - V228C
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
Similarity search - Function
Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / 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 / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / 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
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Catalase
Similarity search - Component
Biological speciesMycothermus thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsYuzugullu Karakus, Y. / Balci, S. / Goc, G. / Pearson, A.R. / Yorke, B.
Funding support Turkey, 1items
OrganizationGrant numberCountry
The Scientific and Technological Research Council of Turkey113Z744 Turkey
CitationJournal: To Be Published
Title: CATPO mutant - V228C
Authors: Yuzugullu Karakus, Y. / Balci, S. / Goc, G. / Pearson, A.R. / Yorke, B.
History
DepositionJul 13, 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 2.0Apr 14, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / diffrn / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[1][3] / _diffrn.pdbx_serial_crystal_experiment ..._atom_sites.fract_transf_matrix[1][3] / _diffrn.pdbx_serial_crystal_experiment / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.overall_SU_B / _refine.pdbx_overall_ESU_R / _refine_hist.d_res_low / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)304,11527
Polymers299,0404
Non-polymers5,07523
Water44,8392489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58290 Å2
ΔGint-434 kcal/mol
Surface area72920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.121, 121.080, 185.119
Angle α, β, γ (deg.)90.000, 101.960, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Catalase


Mass: 74760.039 Da / Num. of mol.: 4 / Fragment: UNP residues 22-699 / Mutation: V228C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycothermus thermophilus (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: M4GGR7, catalase
#2: Chemical
ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


Mass: 632.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2489 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
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 / Serial crystal experiment: N
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: 1.45→112.84 Å / Num. obs: 473154 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.085 / Net I/σ(I): 7.4
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 22629 / CC1/2: 0.658 / Rpim(I) all: 0.566 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AUM

4aum


Resolution: 1.47→55.25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.314 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1752 22662 5 %RANDOM
Rwork0.1493 ---
obs0.1505 430890 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.62 Å2 / Biso mean: 13.374 Å2 / Biso min: 4.27 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.01 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.47→55.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21103 0 362 2489 23954
Biso mean--26.11 19.05 -
Num. residues----2709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01323726
X-RAY DIFFRACTIONr_bond_other_d0.0010.01720981
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.65932479
X-RAY DIFFRACTIONr_angle_other_deg1.5571.58348828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03253047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43122.0231369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.627153664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.11115182
X-RAY DIFFRACTIONr_chiral_restr0.0940.22968
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0228060
X-RAY DIFFRACTIONr_gen_planes_other0.0050.025434
LS refinement shellResolution: 1.47→1.508 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 1711 -
Rwork0.255 31778 -
all-33489 -
obs--99.45 %

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