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- PDB-5v4o: Crystal structure of the D141A/Q233E/N240D variant of catalase-pe... -

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Basic information

Entry
Database: PDB / ID: 5v4o
TitleCrystal structure of the D141A/Q233E/N240D variant of catalase-peroxidase from B. pseudomallei
ComponentsCatalase-peroxidase
KeywordsOXIDOREDUCTASE / catalase / peroxidase / D141A/Q233E/N240D / 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: 1.95 Å
AuthorsLoewen, P.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and ENgineering Research CouncilD9600 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
DepositionMar 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Feb 1, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_PDB_obs_spr ...database_2 / pdbx_database_PDB_obs_spr / 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 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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 1.4Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)161,05914
Polymers159,0542
Non-polymers2,00612
Water19,7441096
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-138 kcal/mol
Surface area50760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.828, 115.454, 175.577
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: 79526.945 Da / Num. of mol.: 2 / Mutation: D141A, Q233E, N240D
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 , 6 types, 1108 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-OXY / OXYGEN MOLECULE


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1096 / 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: 3.28 Å3/Da / Density % sol: 62.48 % / Mosaicity: 0.21 °
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: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→46.201 Å / Num. all: 141391 / Num. obs: 141391 / % possible obs: 95 % / Redundancy: 3.4 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.086 / Rsym value: 0.074 / Net I/av σ(I): 8.2 / Net I/σ(I): 9.8 / Num. measured all: 485977
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRpim(I) allRrim(I) allRsym value% possible all
1.95-2.063.40.4381.7210060.2620.5140.43897.3
2.06-2.183.40.2952.50.1740.3440.29596.8
2.18-2.333.40.2093.60.1230.2440.20996.5
2.33-2.523.40.1455.10.0850.1690.14595.9
2.52-2.763.50.116.80.0640.1280.1195.3
2.76-3.083.50.0890.0460.0930.0894.5
3.08-3.563.50.05811.40.0330.0670.05893.1
3.56-4.363.50.04713.80.0270.0540.04791.4
4.36-6.173.50.0415.80.0220.0460.0490.3
6.17-46.2013.50.02822.10.0170.0330.02888.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MWV

1mwv
PDB Unreleased entry


Resolution: 1.95→46.201 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.911 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.111 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 7043 5 %RANDOM
Rwork0.1495 ---
obs0.1511 134265 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.51 Å2 / Biso mean: 31.481 Å2 / Biso min: 17.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2--2.27 Å20 Å2
3----1.42 Å2
Refinement stepCycle: final / Resolution: 1.95→46.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11006 0 134 1096 12236
Biso mean--39.41 36.91 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.01911518
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210426
X-RAY DIFFRACTIONr_angle_refined_deg2.1361.95315682
X-RAY DIFFRACTIONr_angle_other_deg1.148324066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22551440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18523.618539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.986151748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7761589
X-RAY DIFFRACTIONr_chiral_restr0.1410.21653
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02113125
X-RAY DIFFRACTIONr_gen_planes_other0.010.022527
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A42900.07
12B42900.07
21A413240.06
22B413240.06
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 545 -
Rwork0.248 10093 -
all-10638 -
obs--97.14 %
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)
10.0184-0.0014-0.02090.13760.06970.20490.00620.0084-0.01580.0081-0.0027-0.02810.02120.0148-0.00350.00620.0052-0.00730.0755-0.00650.0209-24.4388-62.0548-21.1705
20.1293-0.00150.02020.0215-0.02910.0895-0.0222-0.00620.00150.00430.0184-0.0096-0.00670.00770.00380.0161-0.0097-0.0120.0730.00350.0163-9.5531-33.28795.5556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 728
2X-RAY DIFFRACTION2B36 - 748

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