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- PDB-2z71: Structure of truncated mutant CYS1GLY of penicillin V acylase fro... -

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Basic information

Entry
Database: PDB / ID: 2z71
TitleStructure of truncated mutant CYS1GLY of penicillin V acylase from bacillus sphaericus co-crystallized with penicillin V
ComponentsPenicillin acylase
KeywordsHYDROLASE / ZYMOGEN / PRECURSOR / PENICILLIN / AUTOPROTEOLYSIS / ANTIBIOTIC RESISTANCE / CATALYSIS / PENICILLIN V ACYLASE
Function / homology
Function and homology information


penicillin amidase activity / penicillin amidase / 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
Chem-PNV / Penicillin V acylase
Similarity search - Component
Biological speciesBacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
Citation
Journal: To be published
Title: Studies on the catalysis and post translational processing of penicillin V acylase
Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
#1: Journal: To be Published
Title: Auto-proteolytic processing of Penicillin V Acylase is simpler than of other related Ntn hydrolases
Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
#2: Journal: To be Published
Title: Co-crystal structure of Penicillin V Acylase with substrate Penicillin V: Insight in to catalytic specificity
Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
#3: Journal: To be Published
Title: Polymorphism shown by the crystals of Penicillin V Acyalse from Bacillus sphaericus
Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
History
DepositionAug 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin acylase
C: Penicillin acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0994
Polymers74,3982
Non-polymers7012
Water91951
1
A: Penicillin acylase
C: Penicillin acylase
hetero molecules

A: Penicillin acylase
C: Penicillin acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1988
Polymers148,7964
Non-polymers1,4024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area21580 Å2
ΔGint-122 kcal/mol
Surface area44970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.730, 158.890, 90.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Penicillin acylase / Penicillin V amidase / PVA


Mass: 37199.105 Da / Num. of mol.: 2 / Mutation: C1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sphaericus (bacteria) / Strain: NCIM 2478 / Production host: Escherichia coli (E. coli) / References: UniProt: P12256, penicillin amidase
#2: Chemical ChemComp-PNV / (2S,5R,6R)-3,3-DIMETHYL-7-OXO-6-(2-PHENOXYACETAMIDO)-4-THIA-1- AZABICYCLO(3.2.0)HEPTANE-2-CARBOXYLIC ACID / PENICILLIN V


Mass: 350.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4 / Details: pH 6.4, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorDate: Mar 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 78639 / Num. obs: 28157 / % possible obs: 89.6 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVA

2pva


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.545 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.743 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 1320 5.1 %RANDOM
Rwork0.23881 ---
obs0.24045 24808 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.447 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20 Å2
2---9.21 Å20 Å2
3---11.79 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5161 0 48 51 5260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0540.0225251
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.9577139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5915659
X-RAY DIFFRACTIONr_chiral_restr0.1780.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.023953
X-RAY DIFFRACTIONr_nbd_refined0.2860.22565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2206
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.25
X-RAY DIFFRACTIONr_mcbond_it1.7171.53278
X-RAY DIFFRACTIONr_mcangle_it2.68225328
X-RAY DIFFRACTIONr_scbond_it4.01931973
X-RAY DIFFRACTIONr_scangle_it5.5474.51811
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.368 76
Rwork0.31 1362

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