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- PDB-3pva: PENICILLIN V ACYLASE FROM B. SPHAERICUS -

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Basic information

Entry
Database: PDB / ID: 3pva
TitlePENICILLIN V ACYLASE FROM B. SPHAERICUS
ComponentsPROTEIN (PENICILLIN 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
Biological speciesLysinibacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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: BNL / Processing site: RCSB
Revision 1.0Nov 15, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 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: PROTEIN (PENICILLIN V ACYLASE)
B: PROTEIN (PENICILLIN V ACYLASE)
C: PROTEIN (PENICILLIN V ACYLASE)
D: PROTEIN (PENICILLIN V ACYLASE)
E: PROTEIN (PENICILLIN V ACYLASE)
F: PROTEIN (PENICILLIN V ACYLASE)
G: PROTEIN (PENICILLIN V ACYLASE)
H: PROTEIN (PENICILLIN V ACYLASE)


Theoretical massNumber of molelcules
Total (without water)297,5138
Polymers297,5138
Non-polymers00
Water50,4422800
1
A: PROTEIN (PENICILLIN V ACYLASE)
B: PROTEIN (PENICILLIN V ACYLASE)
C: PROTEIN (PENICILLIN V ACYLASE)
D: PROTEIN (PENICILLIN V ACYLASE)


Theoretical massNumber of molelcules
Total (without water)148,7564
Polymers148,7564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19230 Å2
ΔGint-128 kcal/mol
Surface area45480 Å2
MethodPISA, PQS
2
E: PROTEIN (PENICILLIN V ACYLASE)
F: PROTEIN (PENICILLIN V ACYLASE)
G: PROTEIN (PENICILLIN V ACYLASE)
H: PROTEIN (PENICILLIN V ACYLASE)


Theoretical massNumber of molelcules
Total (without water)148,7564
Polymers148,7564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19250 Å2
ΔGint-129 kcal/mol
Surface area45510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.400, 129.600, 156.700
Angle α, β, γ (deg.)88.30, 83.40, 84.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PROTEIN (PENICILLIN V ACYLASE) / PENICILLIN V AMIDASE


Mass: 37189.105 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Lysinibacillus sphaericus (bacteria) / References: UniProt: P12256, penicillin amidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2800 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
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-IDDetails
10.1 Msodium phosphate1reservoirpH6.4
23 mMdithiothreitol1reservoir
40.9 %(w/v)sucrose solution1reservoir
515 mg/mlprotain1drop
60.2 Msodium phosphate1drop
3ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→18 Å / Num. obs: 77056 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.2
Reflection
*PLUS
Num. measured all: 111412

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED STRUCTURE FROM HEXAGONAL FORM

Resolution: 2.8→14 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.243 3858 5 %
Rwork0.211 --
obs-72876 85 %
Displacement parametersBiso mean: 56.6 Å2
Refinement stepCycle: LAST / Resolution: 2.8→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20840 0 0 2800 23640
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_d
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
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 14 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 56.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04

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