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- PDB-4n92: Crystal structure of beta-lactamse PenP_E166S -

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Basic information

Entry
Database: PDB / ID: 4n92
TitleCrystal structure of beta-lactamse PenP_E166S
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsPan, X. / Wong, W. / Zhao, Y.
CitationJournal: Biochemistry / Year: 2014
Title: Perturbing the General Base Residue Glu166 in the Active Site of Class A beta-Lactamase Leads to Enhanced Carbapenem Binding and Acylation
Authors: Pan, X. / Wong, W. / He, Y. / Jiang, Y. / Zhao, Y.
History
DepositionOct 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

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Assembly

Deposited unit
B: Beta-lactamase
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)59,5722
Polymers59,5722
Non-polymers00
Water7,656425
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.310, 46.190, 66.280
Angle α, β, γ (deg.)78.430, 75.710, 69.360
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-lactamase / / Penicillinase


Mass: 29785.766 Da / Num. of mol.: 2 / Fragment: Small exopenicillinase / Mutation: E166S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: blaP, penP, penP blaP / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00808, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, PEG 3350, ammonium acetate, pH 8.0, vapor diffusion, hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 19, 2013
RadiationMonochromator: VARIMAX SYSTEM BY OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→42.88 Å / Num. all: 32459 / Num. obs: 32459 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→42.88 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.874 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1647 5.1 %RANDOM
Rwork0.1768 ---
obs0.1796 32453 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.32 Å2 / Biso mean: 16.556 Å2 / Biso min: 6.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20.01 Å2
2--0.03 Å20.04 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.93→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 0 425 4425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024176
X-RAY DIFFRACTIONr_bond_other_d0.0090.024120
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.9815670
X-RAY DIFFRACTIONr_angle_other_deg0.99439522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78525.155194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76615780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91530
X-RAY DIFFRACTIONr_chiral_restr0.3010.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
X-RAY DIFFRACTIONr_mcbond_it1.2791.4192078
X-RAY DIFFRACTIONr_mcbond_other1.2721.4182077
X-RAY DIFFRACTIONr_mcangle_it1.9612.1152588
LS refinement shellResolution: 1.926→1.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 115 -
Rwork0.232 2045 -
all-2160 -
obs--84.01 %

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