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- PDB-3pl1: Determination of the crystal structure of the pyrazinamidase from... -

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Basic information

Entry
Database: PDB / ID: 3pl1
TitleDetermination of the crystal structure of the pyrazinamidase from M.tuberculosis : a structure-function analysis for prediction resistance to pyrazinamide.
ComponentsPYRAZINAMIDASE/NICOTINAMIDASE PNCA (PZase)
KeywordsHYDROLASE / Rossmann fold / nicotinamidase-pyrazinamidase / resistance to pyrazinamide
Function / homology
Function and homology information


nicotinamidase activity / NAD salvage / antibiotic metabolic process / nicotinamide metabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / manganese ion binding / iron ion binding
Similarity search - Function
Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Bifunctional pyrazinamidase/nicotinamidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPetrella, S. / Gelus-Ziental, N. / Mayer, C. / Sougakoff, W.
CitationJournal: Plos One / Year: 2011
Title: Crystal Structure of the Pyrazinamidase of Mycobacterium tuberculosis: Insights into Natural and Acquired Resistance to Pyrazinamide.
Authors: Petrella, S. / Gelus-Ziental, N. / Maudry, A. / Laurans, C. / Boudjelloul, R. / Sougakoff, W.
History
DepositionNov 12, 2010Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 12, 2011ID: 3GBC
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 1, 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_site
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_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_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: PYRAZINAMIDASE/NICOTINAMIDASE PNCA (PZase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6772
Polymers19,6221
Non-polymers561
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.100, 84.100, 100.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein PYRAZINAMIDASE/NICOTINAMIDASE PNCA (PZase) / Pyrazinamidase / Pyrazinamidase/nicotinamidase


Mass: 19621.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2103, pncA, Rv2043c / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q50575, nicotinamidase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 1.6M Sulfate de Magnesium, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→42.3 Å / Num. obs: 11014 / % possible obs: 92.9 % / Redundancy: 11.6 %
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1260 / Rsym value: 0.498 / % possible all: 72.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IM5

1im5


Resolution: 2.2→42.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.46 / SU B: 12.779 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23996 551 5 %RANDOM
Rwork0.1945 ---
obs0.19679 10463 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.44 Å2 / Biso mean: 45.08 Å2 / Biso min: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 1 44 1417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1181.9361915
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1825184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04124.12763
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88515195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.402158
X-RAY DIFFRACTIONr_chiral_restr0.160.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.2546
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2934
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.217
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3831.5947
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23521463
X-RAY DIFFRACTIONr_scbond_it3.8293526
X-RAY DIFFRACTIONr_scangle_it5.6984.5452
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 36 -
Rwork0.297 681 -
all-717 -
obs-681 100 %
Refinement TLS params.Method: refined / Origin x: 2.7725 Å / Origin y: -29.1249 Å / Origin z: 2.1104 Å
111213212223313233
T0.0582 Å2-0.0244 Å2-0.0447 Å2-0.0996 Å20.0335 Å2--0.0514 Å2
L2.1029 °2-0.2108 °20.8936 °2-2.2849 °2-0.336 °2--1.583 °2
S-0.0742 Å °-0.1081 Å °-0.0122 Å °0.0333 Å °0.1912 Å °0.0971 Å °-0.029 Å °-0.178 Å °-0.117 Å °

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