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- PDB-2oqc: Crystal Structure of Penicillin V acylase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2oqc
TitleCrystal Structure of Penicillin V acylase from Bacillus subtilis
ComponentsPenicillin V acylase
KeywordsHYDROLASE / NTN-HYDROLASE / PENICILLIN V ACYLASE / CONJUGATED BILE ACID HYDROLASE / CHOLOYLGLYCINE HYDROLASE / BACILLUS SUBTILIS
Function / homology
Function and homology information


penicillin amidase / hydrolase 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
Penicillin V acylase / Penicillin V acylase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSuresh, C.G. / Rathinaswamy, P. / Pundle, A.V. / Prabhune, A.A. / Sivaraman, H. / Brannigan, J.A. / Dodson, G.G.
Citation
Journal: to be published
Title: Crystal Structure of Penicillin V acylase from Bacillus subtilis
Authors: Suresh, C.G. / Rathinaswamy, P. / Pundle, A.V. / Prabhune, A.A. / Sivaraman, H. / Brannigan, J.A. / Dodson, G.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Cloning, purification, crystallization and preliminary structural studies of penicillin V acylase from Bacillus subtilis
Authors: Rathinaswamy, P. / Pundle, A.V. / Prabhune, A.A. / Sivaraman, H. / Brannigan, J.A. / Dodson, G.G. / Suresh, C.G.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Apr 16, 2014Group: Other
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin V acylase
B: Penicillin V acylase


Theoretical massNumber of molelcules
Total (without water)74,0782
Polymers74,0782
Non-polymers00
Water7,566420
1
A: Penicillin V acylase
B: Penicillin V acylase

A: Penicillin V acylase
B: Penicillin V acylase


Theoretical massNumber of molelcules
Total (without water)148,1554
Polymers148,1554
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area16730 Å2
ΔGint-69 kcal/mol
Surface area45610 Å2
MethodPISA
2
A: Penicillin V acylase

A: Penicillin V acylase


Theoretical massNumber of molelcules
Total (without water)74,0782
Polymers74,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
MethodPQS
3
B: Penicillin V acylase

B: Penicillin V acylase


Theoretical massNumber of molelcules
Total (without water)74,0782
Polymers74,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
MethodPQS
Unit cell
Length a, b, c (Å)110.963, 307.956, 56.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 4 / Auth seq-ID: 1 - 329 / Label seq-ID: 1 - 327

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Penicillin V acylase


Mass: 37038.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: IG20 / Gene: yxeI / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2HPP6, UniProt: P54948*PLUS, penicillin amidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 4M sodium formate in 100mM Tris-HCl buffer, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 7, 2002 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.497→20 Å / Num. obs: 31859 / Biso Wilson estimate: 40.76 Å2
Reflection shellResolution: 2.497→2.562 Å / % possible all: 96.24

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PVA

2pva


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.252 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 1705 5.1 %RANDOM
Rwork0.15466 ---
obs0.15785 31859 98.65 %-
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: 40.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---3.35 Å20 Å2
3---3.34 Å2
Refine analyze
FreeObs
Luzzati sigma a0.231 Å0.296 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 0 420 5502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0225198
X-RAY DIFFRACTIONr_angle_refined_deg2.3411.957056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4245626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.70824.219256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57915868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9091530
X-RAY DIFFRACTIONr_chiral_restr0.1820.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023972
X-RAY DIFFRACTIONr_nbd_refined0.2630.22492
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2399
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.2201
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3960.285
X-RAY DIFFRACTIONr_mcbond_it1.6271.53246
X-RAY DIFFRACTIONr_mcangle_it2.60425102
X-RAY DIFFRACTIONr_scbond_it4.23832239
X-RAY DIFFRACTIONr_scangle_it6.4764.51954
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2541 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.120.5
medium thermal2.242
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 109 -
Rwork0.177 2269 -
obs--96.24 %

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