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- PDB-4n9k: crystal structure of beta-lactamse PenP_E166S in complex with cep... -

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Basic information

Entry
Database: PDB / ID: 4n9k
Titlecrystal structure of beta-lactamse PenP_E166S in complex with cephaloridine
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / hydrolase / HYDROLASE-ANTIBIOTIC complex
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
Chem-CED / Beta-lactamase
Similarity search - Component
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 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,2524
Polymers59,5722
Non-polymers6812
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.370, 45.800, 66.120
Angle α, β, γ (deg.)77.850, 75.410, 69.000
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: Chemical ChemComp-CED / 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / DEGRADED CEPHALORIDINE, open form


Mass: 340.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N2O4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, PEG 3350, ammonium acetate, pH 8.0, 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 25, 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→42.38 Å / Num. all: 31762 / Num. obs: 31754 / % possible obs: 99.97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALAdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→39.73 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.816 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1617 5.1 %RANDOM
Rwork0.1759 30136 --
obs0.1786 31753 92.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.17 Å2 / Biso mean: 15.5234 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2--0.01 Å20.01 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.93→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 44 411 4455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024228
X-RAY DIFFRACTIONr_bond_other_d0.0080.024155
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9925742
X-RAY DIFFRACTIONr_angle_other_deg0.98839602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0475536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95825.179195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51815781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1831530
X-RAY DIFFRACTIONr_chiral_restr0.210.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214765
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02891
X-RAY DIFFRACTIONr_mcbond_it1.2551.3332080
X-RAY DIFFRACTIONr_mcbond_other1.2421.3312079
X-RAY DIFFRACTIONr_mcangle_it1.9371.9852591
LS refinement shellResolution: 1.926→1.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 117 -
Rwork0.216 2037 -
all-2154 -
obs--83.98 %

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