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- PDB-3mji: Activation of catalytic cysteine without a base in a Mutant Penic... -

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Basic information

Entry
Database: PDB / ID: 3mji
TitleActivation of catalytic cysteine without a base in a Mutant Penicillin Acylase Precursor
ComponentsPenicillin acylasePenicillin amidase
KeywordsHYDROLASE / ZYMOGEN / PENICILLIN / AUTOPROTEOLYSIS / ANTIBIOTIC RESISTANCE / CATALYSIS / PENICILLIN V ACYLASE / AMIDASE
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 speciesBacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPathak, M.C. / Suresh, C.G. / Dodson, G.G. / Murshudov, G.N.
Citation
Journal: To be Published
Title: Activation of catalytic cysteine without a base in a Mutant Penicillin Acylase Precursor
Authors: Pathak, M.C. / Suresh, C.G. / Dodson, G.G. / Murshudov, G.N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Cloning, preparation and preliminary crystallographic studies of Penicillin V Acylase autoproteolytic processing mutants
Authors: Chandra, P.M. / Brannigan, J.A. / Prabhune, A. / Pundle, A. / Turkenburg, J.P. / Dodson, G.G. / Suresh, C.G.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin acylase
B: Penicillin acylase
C: Penicillin acylase
D: Penicillin acylase


Theoretical massNumber of molelcules
Total (without water)150,1224
Polymers150,1224
Non-polymers00
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18790 Å2
ΔGint-124 kcal/mol
Surface area44470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.642, 90.089, 102.269
Angle α, β, γ (deg.)90.00, 102.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37530.535 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
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: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.901
11L, -K, H20.099
ReflectionResolution: 2.5→50 Å / Num. obs: 62997 / % possible obs: 99.9 % / Rsym value: 0.086

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.6.0041refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.938 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21122 3216 5.1 %RANDOM
Rwork0.16611 ---
obs0.16839 62981 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.443 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å27.48 Å2
2--11.13 Å20 Å2
3----8.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10410 0 0 319 10729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02210630
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.96514444
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68951330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.0824.825456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.15151806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2991544
X-RAY DIFFRACTIONr_chiral_restr0.1450.21648
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217980
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0470.262353
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 193 -
Rwork0.178 3762 -
obs--84.42 %

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