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- PDB-5l05: Crystal structure of catalase-peroxidase KATG of burkholderia pse... -

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Entry
Database: PDB / ID: 5l05
TitleCrystal structure of catalase-peroxidase KATG of burkholderia pseudomallei treated with INH
ComponentsCatalase-peroxidase
KeywordsOXIDOREDUCTASE / catalase / peroxidase / KatG
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
Peroxidized Heme Form 2 / OXYGEN MOLECULE / Catalase-peroxidase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLoewen, P.C.
CitationJournal: J. Mol. Biol. / Year: 2003
Title: Catalase-peroxidase KatG of Burkholderia pseudomallei at 1.7A resolution.
Authors: Carpena, X. / Loprasert, S. / Mongkolsuk, S. / Switala, J. / Loewen, P.C. / Fita, I.
History
DepositionJul 26, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionAug 24, 2016ID: 1MWV
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: diffrn_source / pdbx_struct_oper_list ...diffrn_source / pdbx_struct_oper_list / software / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.pdbx_keywords
Revision 2.0Mar 28, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_source / pdbx_nonpoly_scheme / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _diffrn_source.pdbx_synchrotron_site / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine_hist.cycle_id / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all
Revision 2.1Oct 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 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)160,83511
Polymers159,0742
Non-polymers1,7619
Water33,8321878
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-81 kcal/mol
Surface area50910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.940, 115.620, 175.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / 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: _ / 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: 79536.984 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: unidentified plasmid (others) / References: UniProt: Q3JNW6, catalase-peroxidase

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Non-polymers , 5 types, 1887 molecules

#2: Chemical ChemComp-HP5 / Peroxidized Heme Form 2


Mass: 648.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O6
#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.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1878 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 62.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16-20% PEG 4K, 20% MPD, 0.1 M SODIUM CITRATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 24, 2002
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.7→96.5 Å / Num. obs: 199550 / % possible obs: 99 % / Redundancy: 3.3 % / Rsym value: 0.073 / Net I/σ(I): 13.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.61 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 11076 / Rsym value: 0.58 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DENZO3.2data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ITK

1itk


Resolution: 1.7→18 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.395 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.176 22115 10 %RANDOM
Rwork0.145 ---
obs0.148 199550 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---1.22 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11010 0 120 1878 13008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.01911506
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210666
X-RAY DIFFRACTIONr_angle_refined_deg2.6891.94715669
X-RAY DIFFRACTIONr_angle_other_deg1.202324444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7951446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02823.603544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.718151755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1641590
X-RAY DIFFRACTIONr_chiral_restr0.1640.21646
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02113337
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022783
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8551.6435724
X-RAY DIFFRACTIONr_mcbond_other1.8541.6435723
X-RAY DIFFRACTIONr_mcangle_it2.6492.4567157
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 46444 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 1586 -
Rwork0.246 14428 -
obs--97.37 %
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)
10.0143-0.018-0.02310.10140.07440.17640.00660.0033-0.0070.00190.0023-0.00550.02580.0209-0.00890.0110.0049-0.00680.0256-0.010.0087-24.5248-62.1637-21.1134
20.1109-0.00120.02780.0292-0.02090.0774-0.0174-0.00760.006-0.00170.0168-0.0121-0.00530.01730.00050.0092-0.0053-0.00440.0294-0.00940.0105-9.688-33.31395.5788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 748
2X-RAY DIFFRACTION1A801 - 805
3X-RAY DIFFRACTION2B36 - 748
4X-RAY DIFFRACTION2B801 - 804

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