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- PDB-5sx7: Crystal structure of catalase-peroxidase KatG of B. pseudomallei ... -

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Basic information

Entry
Database: PDB / ID: 5sx7
TitleCrystal structure of catalase-peroxidase KatG of B. pseudomallei at pH 8.5
ComponentsCatalase-peroxidase
KeywordsOXIDOREDUCTASE / catalase-peroxidase / pH changes / KatG oxidoreductase
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 / 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 Council (NSERC, Canada)D9600 Canada
CitationJournal: Biochemistry / Year: 2006
Title: Roles for Arg426 and Trp111 in the modulation of NADH oxidase activity of the catalase-peroxidase KatG from Burkholderia pseudomallei inferred from pH-induced structural changes.
Authors: Carpena, X. / Wiseman, B. / Deemagarn, T. / Herguedas, B. / Ivancich, A. / Singh, R. / Loewen, P.C. / Fita, I.
History
DepositionAug 9, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionAug 31, 2016ID: 2FXJ
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Structure summary
Category: pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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.pdbx_ptnr1_label_alt_id / _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 1.4Nov 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)161,44216
Polymers159,1382
Non-polymers2,30414
Water26,5181472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint-108 kcal/mol
Surface area49330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.413, 114.948, 173.998
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: 79568.984 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JNW6, catalase-peroxidase

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Non-polymers , 6 types, 1486 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1472 / 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: 3.16 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16-20% PEG 4000, 20% MPD, pH 5.6 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→95.91 Å / Num. obs: 126909 / % possible obs: 91.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.48 / Net I/σ(I) obs: 2.41 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MWV

1mwv
PDB Unreleased entry


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.995 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 6673 5 %RANDOM
Rwork0.1511 ---
obs0.153 126909 90.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.99 Å2 / Biso mean: 21.356 Å2 / Biso min: 9.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11014 0 156 1472 12642
Biso mean--26.97 30.83 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.01911536
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210725
X-RAY DIFFRACTIONr_angle_refined_deg2.1011.95415688
X-RAY DIFFRACTIONr_angle_other_deg1.146324566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93251426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07723.736546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.904151752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2811587
X-RAY DIFFRACTIONr_chiral_restr0.1420.21656
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02113288
X-RAY DIFFRACTIONr_gen_planes_other0.010.022791
X-RAY DIFFRACTIONr_mcbond_it1.4221.7045712
X-RAY DIFFRACTIONr_mcbond_other1.421.7035709
X-RAY DIFFRACTIONr_mcangle_it2.0922.5487121
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43300.08
12B43300.08
21A420420.06
22B420420.06
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 497 -
Rwork0.22 9595 -
all-10092 -
obs--94.15 %
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)
10.0696-0.0288-0.01620.05860.06730.16010.01030.0148-0.03040.0035-0.01140.02030.01440.02340.0010.00990.00240.00050.0188-0.01570.0219-24.2999-61.8278-20.8243
20.16960.00550.0320.032-0.03540.0513-0.0186-0.00830.0030.00150.0013-0.0103-0.00820.00480.01730.0174-0.0018-0.00050.01340.00670.0085-9.7128-32.94265.3762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 807
2X-RAY DIFFRACTION2B36 - 807

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