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- PDB-6cdq: Crystal structure of the W202F variant of catalase-peroxidase fro... -

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Basic information

Entry
Database: PDB / ID: 6cdq
TitleCrystal structure of the W202F variant of catalase-peroxidase from B. pseudomallei with INH bound.
ComponentsCatalase-peroxidase
Keywordsoxidoreductase/oxidoreductase inhibitor / catalase / peroxidase / W202F / heme / INH / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding
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 / pyridine-4-carbohydrazide / OXYGEN MOLECULE / PHOSPHATE ION / Catalase-peroxidase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLoewen, P.C.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)D9600-2012 Canada
Canada Research Chair Program Canada
CitationJournal: To be published
Title: Crystal structure of the W202F variant of catalase-peroxidase from B. pseudomallei with INH bound.
Authors: Loewen, P.C.
History
DepositionFeb 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 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 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 / 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_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 / _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-peroxidase
B: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,29319
Polymers158,9962
Non-polymers2,29717
Water22,9151272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-152 kcal/mol
Surface area49810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.531, 114.896, 174.099
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: 0 / 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: 0 / 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 , 1 types, 2 molecules AB

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


Mass: 79497.953 Da / Num. of mol.: 2 / Mutation: W202F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: katG, BURPS1710b_3366 / Plasmid: pKS / Production host: Escherichia coli (E. coli) / Strain (production host): UM262 / References: UniProt: Q3JNW6, catalase-peroxidase

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Non-polymers , 8 types, 1289 molecules

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


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 / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 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-NIZ / pyridine-4-carbohydrazide / isonicotinic acid hydrazid / Isoniazid


Mass: 137.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7N3O / Comment: antibiotic*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1272 / 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: 3.23 Å3/Da / Density % sol: 61.88 % / Mosaicity: 0.14 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: MPD, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 30, 2017 / 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: 1.92→174.099 Å / Num. all: 136130 / Num. obs: 136130 / % possible obs: 88.8 % / Redundancy: 3.3 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.093 / Rsym value: 0.078 / Net I/av σ(I): 6.6 / Net I/σ(I): 9.4 / Num. measured all: 445240
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.92-2.023.20.5161.5215730.3310.6180.51697.3
2.02-2.153.10.3122.4198890.2040.3760.31294.3
2.15-2.293.20.2053.7176940.130.2440.20589.6
2.29-2.483.30.1375.3164790.0850.1630.13789.4
2.48-2.723.30.0997.1148050.0620.1180.09987.1
2.72-3.043.20.0758.6132410.0470.0890.07586.1
3.04-3.513.40.05810113020.0350.0680.05882.9
3.51-4.293.50.04611.299850.0270.0540.04686.1
4.29-6.073.40.04611.471970.0280.0540.04679.3
6.07-48.2933.60.04610.639650.0250.0520.04676.5

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1MWV

1mwv
PDB Unreleased entry


Resolution: 1.92→174.099 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.932 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.126 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 6845 5 %RANDOM
Rwork0.1659 ---
obs0.1676 129234 88.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.43 Å2 / Biso mean: 26.538 Å2 / Biso min: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--1.62 Å20 Å2
3----1.03 Å2
Refinement stepCycle: final / Resolution: 1.92→174.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11004 0 152 1272 12428
Biso mean--31.26 33.23 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01911534
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210402
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9515697
X-RAY DIFFRACTIONr_angle_other_deg0.764324017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70851442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54423.665543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.022151750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7491588
X-RAY DIFFRACTIONr_chiral_restr0.1010.21649
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02113195
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022545
Refine LS restraints NCS

Ens-ID: 1 / Number: 47634 / 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: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 559 -
Rwork0.278 10478 -
all-11037 -
obs--97.55 %
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)
10.0041-0.0011-0.01450.12060.07870.2189-0.00060.0067-0.01030.00890.0038-0.01330.03590.023-0.00320.00710.00920.00180.0354-0.01050.0813-24.375-61.959-20.896
20.1222-0.01090.03460.0222-0.03320.1241-0.02410.0004-0.00030.00370.0163-0.0165-0.0130.0160.00780.0074-0.0038-0.01230.0362-0.00540.0833-9.501-33.0835.528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 748
2X-RAY DIFFRACTION1A801 - 809
3X-RAY DIFFRACTION2B36 - 748
4X-RAY DIFFRACTION2B801 - 808

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