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- PDB-5kq0: Crystal structure of the A290D variant of catalase-peroxidase fro... -

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Basic information

Entry
Database: PDB / ID: 5kq0
TitleCrystal structure of the A290D variant of catalase-peroxidase from B. pseudomallei
ComponentsCatalase-peroxidase
KeywordsOXIDOREDUCTASE / catalase / peroxidase / A290D / heme
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 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase ...Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / 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
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLoewen, P.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)D9600 Canada
CitationJournal: Biochemistry / Year: 2017
Title: The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine.
Authors: Machuqueiro, M. / Victor, B. / Switala, J. / Villanueva, J. / Rovira, C. / Fita, I. / Loewen, P.C.
History
DepositionJul 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)161,30216
Polymers159,2262
Non-polymers2,07614
Water29,2741625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint-168 kcal/mol
Surface area49970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.760, 113.490, 174.513
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
12A
22B

NCS domain segments:

Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA36 - 11016 - 90
21GLYGLYBB36 - 11016 - 90
12HISHISAA112 - 74892 - 728
22HISHISBB112 - 74892 - 728

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 79612.992 Da / Num. of mol.: 2 / Mutation: A290D
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 , 7 types, 1639 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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1625 / 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: 3.2 Å3/Da / Density % sol: 61.53 % / Mosaicity: 0.24 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97944 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2015 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 1.8→95.141 Å / Num. obs: 181938 / % possible obs: 98.7 % / Redundancy: 2.9 % / Rsym value: 0.059 / Net I/av σ(I): 10.862 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.92.90.4741.6199.5
1.9-2.012.90.3042.5199.5
2.01-2.152.90.1973.4199.4
2.15-2.322.90.145.1199.3
2.32-2.552.90.0947.9199.1
2.55-2.852.90.06810.9198.8
2.85-3.292.90.04416198.3
3.29-4.022.90.03120.8197.5
4.02-5.6930.02426.2196.7
5.69-44.52330.02224.9193.1

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MWV

1mwv
PDB Unreleased entry


Resolution: 1.8→95.14 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.657 / SU ML: 0.073 / SU R Cruickshank DPI: 0.0911 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.093 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1848 9088 5 %RANDOM
Rwork0.1519 ---
obs0.1535 172743 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.17 Å2 / Biso mean: 25.069 Å2 / Biso min: 13.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2--2.51 Å20 Å2
3----1.06 Å2
Refinement stepCycle: final / Resolution: 1.8→95.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11020 0 136 1625 12781
Biso mean--31.1 33.85 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.01911561
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210708
X-RAY DIFFRACTIONr_angle_refined_deg2.2661.95315736
X-RAY DIFFRACTIONr_angle_other_deg1.193324536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03651444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67223.688545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71151756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5451589
X-RAY DIFFRACTIONr_chiral_restr0.1640.21655
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02113404
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022805
X-RAY DIFFRACTIONr_mcbond_it1.8771.9585753
X-RAY DIFFRACTIONr_mcbond_other1.8711.9575752
X-RAY DIFFRACTIONr_mcangle_it2.6712.9267193
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43680.08
12B43680.08
21A420820.07
22B420820.07
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 696 -
Rwork0.236 12722 -
all-13418 -
obs--99.39 %
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)
10.0209-0.0226-0.03180.08970.06290.13330.00630.0055-0.01610.0012-0.0122-0.01060.0205-0.00550.00590.0361-0.00290.00790.0039-0.00670.0397-24.2286-61.3936-21.5248
20.0952-0.01620.02480.0197-0.0220.0919-0.0159-0.01570.0072-0.00580.0068-0.0216-0.0052-0.0010.00910.0409-0.0071-0.00620.0057-0.00380.0371-9.2042-32.64435.2598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 808
2X-RAY DIFFRACTION2B36 - 806

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