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- PDB-1im5: Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in C... -

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Basic information

Entry
Database: PDB / ID: 1im5
TitleCrystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc
Components180aa long hypothetical Pyrazinamidase/Nicotinamidase
KeywordsHYDROLASE / pyrazinamidase / pyrazinamide / nicotinamidase / tuberculosis / PZA resistance / drug resistance / metal ion catalysis / cysteine hydrolase / amidase / covalent catalysis
Function / homology
Function and homology information


pyridine nucleotide biosynthetic process / nicotinamidase / hydrolase activity, acting on carbon-nitrogen (but not 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
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDu, X. / Kim, S.-H.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure and mechanism of catalysis of a pyrazinamidase from Pyrococcus horikoshii.
Authors: Du, X. / Wang, W. / Kim, R. / Yakota, H. / Nguyen, H. / Kim, S.H.
History
DepositionMay 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 180aa long hypothetical Pyrazinamidase/Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2882
Polymers20,2221
Non-polymers651
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.978, 43.266, 55.553
Angle α, β, γ (deg.)90.00, 101.34, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer is biologically active

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Components

#1: Protein 180aa long hypothetical Pyrazinamidase/Nicotinamidase


Mass: 20222.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH 999 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)/SJS1244 / References: UniProt: O58727, nicotinamidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.6424.9
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop4.627.5% peg 3350, 100mM sodium acetate, pH 4.6, 250 mM ammonium acetate, 8% glycerol. Seeding., VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop4.6peg 3350, ammonium acetate, sodium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
31 mMEDTA1drop
4100 mMsodium acetate1reservoirpH4.6
5250 mMammonium acetate1reservoir
65 mM1reservoirZnCl2
78 %glycerol1reservoir
827.5 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 24, 2000 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 18550 / Num. obs: 18049 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.11 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 37.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2.02 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 25.5 / Num. unique all: 753 / % possible all: 81.9
Reflection shell
*PLUS
% possible obs: 81.9 %

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Processing

Software
NameVersionClassification
SHELXL-97refinement
CNSrefinement
SOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a structure obtained on MAD data

Resolution: 1.65→20 Å / Num. parameters: 14202 / Num. restraintsaints: 17019 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1775 -RANDOM
Rwork0.1527 ---
all0.1529 18533 --
obs0.1529 17977 97 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1552
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 1 128 1566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.6 % / Rfactor all: 0.153 / Rfactor Rfree: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.1
X-RAY DIFFRACTIONs_plane_restr0.025
X-RAY DIFFRACTIONs_chiral_restr0.03

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