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

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Basic information

Entry
Database: PDB / ID: 2ccd
TitleCrystal structure of the catalase-peroxidase (KatG) and S315T mutant from Mycobacterium tuberculosis
ComponentsPEROXIDASE/CATALASE T
KeywordsOXIDOREDUCTASE / KATG / HYDROGEN PEROXIDE / IRON / METAL-BINDING
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: 2.1 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 1.1Jul 13, 2011Group: Advisory / 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 / struct_conn
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 / _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

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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)162,6364
Polymers161,4032
Non-polymers1,2332
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-103.6 kcal/mol
Surface area49470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.807, 149.807, 154.493
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
1111A26 - 741
2111B26 - 741

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Components

#1: Protein PEROXIDASE/CATALASE T / KATG S315T / CATALASE-PEROXIDASE T


Mass: 80701.633 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HEME PROTORPHYRIN IX FE(III) / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: MTB H37RV / Plasmid: PSY31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): UM262 / References: UniProt: Q08129, UniProt: P9WIE5*PLUS
#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.: 595 / 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 ENGINEERED RESIDUE IN CHAIN A, SER 315 TO THR ENGINEERED RESIDUE IN CHAIN B, SER 315 TO THR

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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: ALS / Beamline: 8.2.1 / Wavelength: 0.974
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 76312 / % possible obs: 78.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.9 / % possible all: 64

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
XTALVIEWphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CC4

2cc4
PDB Unreleased entry


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.862 / SU B: 17.759 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 3986 5 %RANDOM
Rwork0.23 ---
obs0.232 76312 78.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---1.5 Å20 Å2
3---2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11034 0 86 595 11715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.97215590
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9651422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85424.023512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.057151754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2741572
X-RAY DIFFRACTIONr_chiral_restr0.0920.21626
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.26193
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.27844
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2818
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.57211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.796211326
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33834898
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9424.54260
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 / Number: 5517 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.380.05
tight thermal1.470.5
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 231
Rwork0.321 4471
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)
10.55460.02510.24270.03950.12330.43540.05410.0188-0.15370.0742-0.0599-0.00640.0041-0.01490.00580.0096-0.0453-0.01020.0120.0274-0.025357.94518.61139.868
20.5587-0.0290.0710.20630.04510.13830.0391-0.03920.02150.0131-0.0187-0.06820.0106-0.0225-0.02040.0112-0.0117-0.02550.0046-0.0043-0.036679.7339.03647.808
30.4390.14140.15111.1168-0.00760.1644-0.03880.046-0.027-0.0650.0215-0.0427-0.0118-0.01890.01740.0268-0.00380.00680.04620.0109-0.140157.17533.50615.047
40.57960.31220.00280.68950.00380.06310.0413-0.0287-0.11990.0006-0.0531-0.0928-0.0201-0.02270.0119-0.0049-0.0051-0.0033-0.00910.0164-0.029840.078-5.5532.776
51.46640.62720.13580.72360.21560.19080.1222-0.2609-0.01070.127-0.17620.02750.0072-0.09290.0540.051-0.07070.01690.1084-0.0148-0.156538.71922.57761.367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 60
2X-RAY DIFFRACTION1B26 - 60
3X-RAY DIFFRACTION2A61 - 433
4X-RAY DIFFRACTION2A1741
5X-RAY DIFFRACTION3A434 - 740
6X-RAY DIFFRACTION4B61 - 433
7X-RAY DIFFRACTION4B1741
8X-RAY DIFFRACTION5B434 - 740

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