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- PDB-2pva: OXIDIZED PENICILLIN V ACYLASE FROM B. SPHAERICUS -

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Basic information

Entry
Database: PDB / ID: 2pva
TitleOXIDIZED PENICILLIN V ACYLASE FROM B. SPHAERICUS
ComponentsPENICILLIN V ACYLASE
KeywordsHYDROLASE / AMIDOHYDROLASE / NTN HYDROLASE / PENICILLIN V ACYLASE
Function / homology
Function and homology information


penicillin amidase / penicillin amidase activity / response to antibiotic
Similarity search - Function
Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DITHIANE DIOL / Penicillin V acylase
Similarity search - Component
Biological speciesLysinibacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsSuresh, C.G. / Pundle, A.V. / Rao, K.N. / SivaRaman, H. / Brannigan, J.A. / McVey, C.E. / Verma, C.S. / Dauter, Z. / Dodson, E.J. / Dodson, G.G.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Penicillin V acylase crystal structure reveals new Ntn-hydrolase family members.
Authors: Suresh, C.G. / Pundle, A.V. / SivaRaman, H. / Rao, K.N. / Brannigan, J.A. / McVey, C.E. / Verma, C.S. / Dauter, Z. / Dodson, E.J. / Dodson, G.G.
History
DepositionNov 13, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 11, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: PENICILLIN V ACYLASE
B: PENICILLIN V ACYLASE
C: PENICILLIN V ACYLASE
D: PENICILLIN V ACYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,9308
Polymers153,3214
Non-polymers6094
Water14,502805
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20550 Å2
ΔGint-129 kcal/mol
Surface area44420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.400, 208.400, 96.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
PENICILLIN V ACYLASE / PENICILLIN V AMIDASE


Mass: 38330.281 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Lysinibacillus sphaericus (bacteria) / References: UniProt: P12256, penicillin amidase
#2: Chemical
ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 3.93 Å3/Da / Density % sol: 68.71 %
Crystal growpH: 6.4
Details: 5MM DTT, 30% AS, 1% SUCROSE, 0.2M NA PHOSPHATE, PH 6.4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
20.2 M1dropNa2HPO4
30.2 Msodium phosphate1reservoirpH6.4
45 mMdithiothreitol1reservoir
610 %(w/v)sucrose1reservoir
5ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 17, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 80217 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14
Reflection
*PLUS
Num. measured all: 239296

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.245 3963 5 %
Rwork0.196 --
obs-75753 97 %
Displacement parametersBiso mean: 57.03 Å2 / Baniso 23: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10372 0 32 805 11209
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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