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- PDB-5txq: Crystal structure of the A143D variant of catalase-peroxidase fro... -

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Basic information

Entry
Database: PDB / ID: 5txq
TitleCrystal structure of the A143D variant of catalase-peroxidase from B. pseudomallei
ComponentsCatalase-peroxidase
KeywordsOXIDOREDUCTASE / catalase / peroxidase / A143D / 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: 1.9 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
DepositionNov 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
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 / 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 1.3Nov 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)160,99512
Polymers159,2262
Non-polymers1,76910
Water26,8421490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-122 kcal/mol
Surface area50280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.670, 115.117, 174.738
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
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, 1500 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.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1490 / 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: 3.24 Å3/Da / Density % sol: 62.09 % / Mosaicity: 0.14 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: 20% MPD, 0.1 M sodium citrate, 17% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2016 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→96.131 Å / Num. all: 159525 / Num. obs: 159525 / % possible obs: 99.8 % / Redundancy: 5 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.086 / Rsym value: 0.077 / Net I/av σ(I): 9.719 / Net I/σ(I): 17.5 / Num. measured all: 791484
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-250.5631.4199.6
2-2.1250.3512.2199.6
2.12-2.2750.2493.1199.7
2.27-2.4550.1714.5199.9
2.45-2.694.90.1216.4199.9
2.69-34.90.0819.51100
3-3.474.90.04716199.9
3.47-4.254.90.0323.61100
4.25-6.0150.02527.21100
6.01-48.0424.70.02227.7199.6

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1MWV

1mwv
PDB Unreleased entry


Resolution: 1.9→96.13 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.965 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.107 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 7899 5 %RANDOM
Rwork0.1566 ---
obs0.1584 151540 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.69 Å2 / Biso mean: 26.768 Å2 / Biso min: 14.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--2.67 Å20 Å2
3----1.57 Å2
Refinement stepCycle: final / Resolution: 1.9→96.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11020 0 118 1490 12628
Biso mean--29.84 33.83 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.01911551
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210690
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.95215721
X-RAY DIFFRACTIONr_angle_other_deg1.18324502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28951446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25223.686548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.659151761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8771590
X-RAY DIFFRACTIONr_chiral_restr0.1540.21650
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02113405
X-RAY DIFFRACTIONr_gen_planes_other0.010.022809
X-RAY DIFFRACTIONr_mcbond_it1.8582.075746
X-RAY DIFFRACTIONr_mcbond_other1.8482.0685745
X-RAY DIFFRACTIONr_mcangle_it2.7313.0957181
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43860.08
12B43860.08
21A421500.06
22B421500.06
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 565 -
Rwork0.263 11071 -
all-11636 -
obs--99.49 %
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)
10.0118-0.0116-0.03770.18890.09070.20110.00290.0071-0.00860.01360.0027-0.07260.0232-0.0081-0.00560.01090.0116-0.00950.0410.00130.05-24.33-61.919-21.254
20.1152-0.01180.00620.016-0.01790.1151-0.015-0.00870.00840.00460.0183-0.0157-0.00220.0139-0.00330.0236-0.0067-0.02450.0404-0.01110.0426-9.454-33.1965.509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 748
2X-RAY DIFFRACTION1A801 - 806
3X-RAY DIFFRACTION2B36 - 748
4X-RAY DIFFRACTION2B801 - 804

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