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- PDB-6mq0: B. pseudomallei KatG crystallized in the presence of furoyl hydrazide -

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Basic information

Entry
Database: PDB / ID: 6mq0
TitleB. pseudomallei KatG crystallized in the presence of furoyl hydrazide
ComponentsCatalase-peroxidase
KeywordsOXIDOREDUCTASE / catalase-peroxidase / heme / furoyl hydrazide
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / response to oxidative stress / 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 MOLECULE / PHOSPHATE ION / Catalase-peroxidase / Catalase-peroxidase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLoewen, P.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)D9600-2012 Canada
CitationJournal: To be published
Title: B. pseudomallei KatG crystallized in the presence of furoyl hydrazide
Authors: Loewen, P.C.
History
DepositionOct 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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
Revision 1.3Oct 30, 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)160,90213
Polymers159,0742
Non-polymers1,82811
Water28,0851559
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-138 kcal/mol
Surface area50050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.460, 115.430, 174.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 79536.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: katG, BOC42_10690, CXQ84_04250, DP46_2227, DP49_6664 / Plasmid: pKS / Production host: Escherichia coli (E. coli) / Strain (production host): UM262
References: UniProt: A0A095KYK6, UniProt: Q939D2*PLUS, catalase-peroxidase

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Non-polymers , 7 types, 1570 molecules

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


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1559 / 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: 3.25 Å3/Da / Density % sol: 62.15 % / Mosaicity: 0.52 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: MPD, 0.1 M sodium citrate, 50 mM furoyl hydrazide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 27, 2009 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→35.209 Å / Num. all: 159840 / Num. obs: 159840 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.109 / Rsym value: 0.098 / Net I/av σ(I): 5.9 / Net I/σ(I): 11 / Num. measured all: 838108
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.9-250.481.5231070.2390.5370.4899.9
2-2.1250.3062.4218720.1510.3420.30699.9
2.12-2.275.20.2183.3206060.1070.2440.21899.9
2.27-2.455.30.1554.8192070.0740.1720.155100
2.45-2.695.40.1245.8177500.0590.1370.124100
2.69-35.40.0947.4160640.0440.1040.094100
3-3.475.40.0757.7142510.0350.0830.075100
3.47-4.255.40.0679.2120970.0320.0740.067100
4.25-6.015.40.069.994790.0280.0660.06100
6.01-35.2095.10.0414.354070.020.0450.0499.5

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1MWV

1mwv
PDB Unreleased entry


Resolution: 1.9→35.209 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.354 / SU ML: 0.067 / SU R Cruickshank DPI: 0.0992 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.097 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 7870 4.9 %RANDOM
Rwork0.1447 ---
obs0.1461 151873 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.42 Å2 / Biso mean: 22.059 Å2 / Biso min: 11.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2--1.56 Å20 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 1.9→35.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10998 0 122 1559 12679
Biso mean--27.29 32.05 -
Num. residues----1424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01311468
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710357
X-RAY DIFFRACTIONr_angle_refined_deg1.531.65315617
X-RAY DIFFRACTIONr_angle_other_deg1.4581.58523925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69451436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16521.797629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.764151748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5341587
X-RAY DIFFRACTIONr_chiral_restr0.080.21419
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0213183
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022596
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 589 -
Rwork0.223 11055 -
all-11644 -
obs--99.85 %
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)
10.0366-0.0221-0.0360.11620.08780.18880.00840.0093-0.0190.0029-0.0041-0.00610.0280.0162-0.00430.01280.0068-0.00620.011-0.01090.0179-24.331-61.989-21.095
20.1364-0.01060.04420.0316-0.01920.0994-0.0182-0.01230.0088-0.00310.0188-0.0162-0.00790.018-0.00060.0093-0.0057-0.0030.0251-0.01190.0139-9.569-33.325.544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 747
2X-RAY DIFFRACTION1A801 - 807
3X-RAY DIFFRACTION2B36 - 747
4X-RAY DIFFRACTION2B801 - 804

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