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- PDB-2cca: Crystal structure of the catalase-peroxidase (KatG) and S315T mut... -

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Basic information

Entry
Database: PDB / ID: 2cca
TitleCrystal structure of the catalase-peroxidase (KatG) and S315T mutant from Mycobacterium tuberculosis
ComponentsPEROXIDASE/CATALASE T
KeywordsOXIDOREDUCTASE / CATALASE-PEROXIDASE / KATG / HEME / PEROXIDASE / HYDROGEN PEROXIDE / IRON / METAL-BINDING / ORGANIC RADICAL
Function / homology
Function and homology information


oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / cell wall / catalase activity / NADPH binding / positive regulation of DNA repair / peptidoglycan-based cell wall / hydrogen peroxide catabolic process ...oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / cell wall / catalase activity / NADPH binding / positive regulation of DNA repair / peptidoglycan-based cell wall / hydrogen peroxide catabolic process / peroxidase activity / cellular response to hydrogen peroxide / response to oxidative stress / response to antibiotic / heme binding / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase-peroxidase / Catalase-peroxidase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYu, H. / Sacchettini, J.C.
CitationJournal: Biochemistry / Year: 2006
Title: Hydrogen Peroxide-Mediated Isoniazid Activation Catalyzed by Mycobacterium Tuberculosis Catalase-Peroxidase (Katg) and its S315T Mutant.
Authors: Zhao, X. / Yu, H. / Yu, S. / Wang, F. / Sacchettini, J.C. / Magliozzo, R.S.
History
DepositionJan 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXIDASE/CATALASE T
B: PEROXIDASE/CATALASE T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,6084
Polymers161,3752
Non-polymers1,2332
Water16,898938
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-102.7 kcal/mol
Surface area49870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.104, 150.104, 153.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A26 - 741
2112B26 - 741

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Components

#1: Protein PEROXIDASE/CATALASE T / KATG / CATALASE-PEROXIDASE T


Mass: 80687.609 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-740
Source method: isolated from a genetically manipulated source
Details: HEME PROTORPHYRIN IX FE(III) / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: MTB H37RV / Plasmid: PKATII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): UM262 / References: UniProt: Q08129, UniProt: P9WIE5*PLUS, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 938 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHAS A DOUBLE FUNCTION: EXHIBITS BOTH A CATALASE AND BROAD- SPECTRUM PEROXIDASE ACTIVITIES. POSSIBLE ...HAS A DOUBLE FUNCTION: EXHIBITS BOTH A CATALASE AND BROAD- SPECTRUM PEROXIDASE ACTIVITIES. POSSIBLE ROLE IN THE INTRACELLULAR SURVIVAL OF MYCOBACTERIA

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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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growpH: 4.6
Details: 6% PEG4000, 0.1M NA ACETATE, PH4.6, 0.17MM N-DODECYL-B-D-MALTOSIDE, PROTEIN CONCENTRATION OF 16MG/ML, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 105049 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.2
Reflection shellResolution: 2→50 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.6 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
CNSphasing
XTALVIEWphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MWV

1mwv
PDB Unreleased entry


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.256 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5847 5 %RANDOM
Rwork0.199 ---
obs0.2 110889 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2---0.87 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11032 0 86 938 12056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02211439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.97415601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0251428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4223.996513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.032151757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1511573
X-RAY DIFFRACTIONr_chiral_restr0.0780.21625
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028953
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.25781
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.27875
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2966
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4041.57271
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.703211333
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96834888
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5764.54264
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2860tight positional0.030.05
2649medium positional0.430.5
2860tight thermal0.10.5
2649medium thermal0.482
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 413
Rwork0.266 7800

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