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- PDB-2wt9: Acinetobacter baumanii nicotinamidase pyrazinamidease -

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Basic information

Entry
Database: PDB / ID: 2wt9
TitleAcinetobacter baumanii nicotinamidase pyrazinamidease
ComponentsNICOTINAMIDASE
KeywordsHYDROLASE / PYRAZINAMIDASE
Function / homology
Function and homology information


nicotinamidase activity / nicotinamidase / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / metal ion binding
Similarity search - Function
Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINIC ACID / Bifunctional protein
Similarity search - Component
Biological speciesACINETOBACTER BAUMANNII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFyfe, P.K. / Rao, V.A. / Zemla, A. / Cameron, S. / Hunter, W.N.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Specificity and Mechanism of Acinetobacter Baumanii Nicotinamidase: Implications for Activation of the Front-Line Tuberculosis Drug Pyrazinamide.
Authors: Fyfe, P.K. / Rao, V.A. / Zemla, A. / Cameron, S. / Hunter, W.N.
History
DepositionSep 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Dec 20, 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: NICOTINAMIDASE
B: NICOTINAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,83611
Polymers51,9982
Non-polymers8389
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-82 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.640, 46.890, 59.480
Angle α, β, γ (deg.)113.19, 88.25, 115.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NICOTINAMIDASE / BIFUNCTIONAL PROTEIN


Mass: 25999.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Strain: AYE / Plasmid: PET15B-TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B0VA03, nicotinamidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.2 Å3/Da / Density % sol: 44.4 % / Description: NONE
Crystal growDetails: 2.0 M AMMONIUM SULPHATE, 200 MM SODIUM CACODYLATE, PH 5.5, 200 MM LITHIUM CHLORIDE AND 20% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.972
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.65→28.4 Å / Num. obs: 47549 / % possible obs: 88.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.25 / % possible all: 75.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IM5

1im5


Resolution: 1.65→28.4 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.131 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2378 5 %RANDOM
Rwork0.179 ---
obs0.182 45170 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.03 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å21.88 Å20.42 Å2
2---0.77 Å2-0.52 Å2
3----2.27 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 50 300 3558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213497
X-RAY DIFFRACTIONr_bond_other_d0.0010.022214
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.9244784
X-RAY DIFFRACTIONr_angle_other_deg1.0532.9985457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61826165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35415544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.286156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024003
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02659
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_it3.18922155
X-RAY DIFFRACTIONr_mcbond_other1.1762874
X-RAY DIFFRACTIONr_mcangle_it4.09633511
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.76221342
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.06931273
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
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 172 -
Rwork0.348 3263 -
obs--100 %

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