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- PDB-5xy4: CATPO mutant - V536W -

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Basic information

Entry
Database: PDB / ID: 5xy4
TitleCATPO mutant - V536W
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
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Catalase
Similarity search - Component
Biological speciesMycothermus thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYuzugullu Karakus, Y. / Goc, G. / Balci, S. / Pearson, A.R. / Yorke, B.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other G113Z744 Turkey
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Identification of the site of oxidase substrate binding in Scytalidium thermophilum catalase.
Authors: Yuzugullu Karakus, Y. / Goc, G. / Balci, S. / Yorke, B.A. / Trinh, C.H. / McPherson, M.J. / Pearson, A.R.
History
DepositionJul 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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
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_ncs_dom_lim
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.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)302,58519
Polymers299,3724
Non-polymers3,21315
Water36,5702030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56010 Å2
ΔGint-416 kcal/mol
Surface area72750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.420, 120.743, 184.653
Angle α, β, γ (deg.)90.00, 102.05, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 21 - 698 / Label seq-ID: 1 - 678

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Catalase


Mass: 74843.109 Da / Num. of mol.: 4 / Fragment: UNP residues 22-699 / Mutation: V536W
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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2030 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 323 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: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→100.37 Å / Num. obs: 252686 / % possible obs: 90 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.047 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11150 / CC1/2: 0.643 / Rpim(I) all: 0.455 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AUM

4aum


Resolution: 1.8→90.46 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.052 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19297 11268 5 %RANDOM
Rwork0.15784 ---
obs0.15961 211910 89.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.712 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å2-0.84 Å2
2--0.79 Å20 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.8→90.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21153 0 193 2030 23376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01422214
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718972
X-RAY DIFFRACTIONr_angle_refined_deg1.781.66930322
X-RAY DIFFRACTIONr_angle_other_deg1.0421.64444495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09652767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90822.1751260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.678153351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.28115155
X-RAY DIFFRACTIONr_chiral_restr0.0850.22818
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0225851
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024425
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3321.86610993
X-RAY DIFFRACTIONr_mcbond_other1.3311.86610992
X-RAY DIFFRACTIONr_mcangle_it1.922.79313785
X-RAY DIFFRACTIONr_mcangle_other1.922.79313786
X-RAY DIFFRACTIONr_scbond_it1.7132.00111221
X-RAY DIFFRACTIONr_scbond_other1.7132.00111221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6032.93916538
X-RAY DIFFRACTIONr_long_range_B_refined4.59423.02926016
X-RAY DIFFRACTIONr_long_range_B_other4.59423.03126017
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A226460.06
12B226460.06
21A225680.06
22C225680.06
31A224140.07
32D224140.07
41B224600.06
42C224600.06
51B224390.06
52D224390.06
61C224240.05
62D224240.05
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 809 -
Rwork0.299 15685 -
obs--90.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3839-0.05420.17540.3943-0.05290.4227-0.00580.17720.0535-0.1419-0.0109-0.0235-0.0560.07030.01670.0647-0.00610.00680.08260.02440.00844.406313.7-71.6087
20.3746-0.01990.17960.33460.01560.4227-0.0265-0.17690.03390.13360.0179-0.0324-0.0621-0.05360.00860.06510.0111-0.01260.0876-0.01560.008414.565512.0945-18.1921
30.4187-0.00980.18710.3564-0.04610.34150.05190.0601-0.0896-0.0943-0.01030.07030.0932-0.0291-0.04150.0447-0.0031-0.02720.0231-0.01530.0328-11.2942-12.846-62.7501
40.4269-0.02840.17790.30610.00720.35410.0409-0.0395-0.08670.0674-0.0022-0.08830.08680.0803-0.03870.03540.0179-0.02920.03750.01070.046731.3005-13.1388-28.8978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 705
2X-RAY DIFFRACTION2B21 - 703
3X-RAY DIFFRACTION3C21 - 704
4X-RAY DIFFRACTION4D21 - 703

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