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- PDB-5sx0: Crystal structure of an oxoferryl species of catalase-peroxidase ... -

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Basic information

Entry
Database: PDB / ID: 5sx0
TitleCrystal structure of an oxoferryl species of catalase-peroxidase KatG at pH7.5
Components(Catalase-peroxidase) x 2
KeywordsOXIDOREDUCTASE / catalase-peroxidase / KatG / compound I / oxoferryl species
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / heme binding / metal ion binding / cytosol
Similarity search - Function
Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / OXYGEN MOLECULE / Catalase-peroxidase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLoewen, P.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)D9600 Canada
CitationJournal: EMBO Rep. / Year: 2005
Title: A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases.
Authors: Carpena, X. / Wiseman, B. / Deemagarn, T. / Singh, R. / Switala, J. / Ivancich, A. / Fita, I. / Loewen, P.C.
History
DepositionAug 9, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionAug 24, 2016ID: 2B2S
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Structure summary
Category: pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase-peroxidase
B: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,09616
Polymers159,0902
Non-polymers2,00614
Water22,0681225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-102 kcal/mol
Surface area50000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.359, 114.886, 174.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 36 - 748 / Label seq-ID: 16 - 728

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Catalase-peroxidase / CP / Peroxidase/catalase


Mass: 79552.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: katG, BURPS1710b_3366 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JNW6, catalase-peroxidase
#2: Protein Catalase-peroxidase / CP / Peroxidase/catalase


Mass: 79536.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: katG, BURPS1710b_3366 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JNW6, catalase-peroxidase

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Non-polymers , 7 types, 1239 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1225 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16-20% MPD, pH 5.6 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.00632 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00632 Å / Relative weight: 1
ReflectionResolution: 2→95.98 Å / Num. obs: 120518 / % possible obs: 98 % / Redundancy: 3.7 % / Rsym value: 0.135 / Net I/σ(I): 7.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.506 / Num. unique all: 13504 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MWV

1mwv
PDB Unreleased entry


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.728 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 13331 10 %RANDOM
Rwork0.1586 ---
obs0.1622 120518 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.36 Å2 / Biso mean: 28.49 Å2 / Biso min: 14.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.61 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11011 0 136 1225 12372
Biso mean--30.84 34.37 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01911481
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210647
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.94915622
X-RAY DIFFRACTIONr_angle_other_deg1.11324392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96351434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55423.678541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.764151741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3361587
X-RAY DIFFRACTIONr_chiral_restr0.1360.21646
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02113286
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022785
X-RAY DIFFRACTIONr_mcbond_it1.8672.2625714
X-RAY DIFFRACTIONr_mcbond_other1.8592.2615712
X-RAY DIFFRACTIONr_mcangle_it2.6833.3797139
Refine LS restraints NCS

Ens-ID: 1 / Number: 47332 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 1011 -
Rwork0.235 9010 -
all-10021 -
obs--99.84 %
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)
10.0283-0.0185-0.0160.12570.06750.17880.00430.0083-0.01880.00080.00660.00340.02290.0253-0.01090.00610.0034-0.00290.0784-0.02130.022-24.431-61.812-21.082
20.1608-0.00780.04390.0356-0.04530.0949-0.0191-0.003-0.00020.00330.0128-0.0151-0.01130.01920.00630.0097-0.0101-0.00360.0664-0.00570.0224-9.651-33.0755.497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 748
2X-RAY DIFFRACTION1A801 - 808
3X-RAY DIFFRACTION2B36 - 748
4X-RAY DIFFRACTION2B801 - 806

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