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- PDB-2quy: Truncated mutant ASN175ALA of penicillin v acylase from bacillus ... -

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Basic information

Entry
Database: PDB / ID: 2quy
TitleTruncated mutant ASN175ALA of penicillin v acylase from bacillus sphaericus
ComponentsPenicillin acylase
KeywordsHYDROLASE / PENICILLIN / AUTOPROTEOLYSIS / NTN / OXY-ANION HOLE / Antibiotic resistance / Zymogen
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
Penicillin V acylase
Similarity search - Component
Biological speciesBacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
CitationJournal: 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.
History
DepositionAug 7, 2007Deposition site: RCSB / 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin acylase
B: Penicillin acylase
C: Penicillin acylase
D: Penicillin acylase
E: Penicillin acylase
F: Penicillin acylase
G: Penicillin acylase
H: Penicillin acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,90116
Polymers297,6178
Non-polymers2848
Water25,2751403
1
A: Penicillin acylase
B: Penicillin acylase
C: Penicillin acylase
D: Penicillin acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,9518
Polymers148,8094
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19180 Å2
ΔGint-168 kcal/mol
Surface area44490 Å2
MethodPISA
2
E: Penicillin acylase
F: Penicillin acylase
G: Penicillin acylase
H: Penicillin acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,9518
Polymers148,8094
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19000 Å2
ΔGint-168 kcal/mol
Surface area44290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.286, 379.383, 102.013
Angle α, β, γ (deg.)90.00, 93.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37202.172 Da / Num. of mol.: 8 / Mutation: N175A
Source method: isolated from a genetically manipulated source
Details: NCIM 2478 / Source: (gene. exp.) Bacillus sphaericus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P12256, penicillin amidase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1403 / 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: 3.07 Å3/Da / Density % sol: 59.92 %
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: ID14-3 / Wavelength: 0.934 Å
DetectorDetector: CCD / Date: Apr 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 370615 / % possible obs: 94.6 % / Rsym value: 0.069

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.074 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20293 18621 5 %RANDOM
Rwork0.17546 ---
obs0.17684 351775 94.25 %-
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: 19.265 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-0.04 Å2
2---0.12 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20584 0 8 1403 21995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02221028
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.95828582
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12852630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.23263
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215796
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.210048
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.21500
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9921.513102
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.717221313
X-RAY DIFFRACTIONr_scbond_it2.82937926
X-RAY DIFFRACTIONr_scangle_it4.5124.57269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.696→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 905
Rwork0.257 17474

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