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- PDB-5zfl: Crystal structure of beta-lactamase PenP mutant E166Y -

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Basic information

Entry
Database: PDB / ID: 5zfl
TitleCrystal structure of beta-lactamase PenP mutant E166Y
ComponentsBeta-lactamase
KeywordsHYDROLASE / class A beta-lactamase / antibiotic resistance
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPan, X. / Zhao, Y.
CitationJournal: Sci Rep / Year: 2020
Title: The hydrolytic water molecule of Class A beta-lactamase relies on the acyl-enzyme intermediate ES* for proper coordination and catalysis.
Authors: He, Y. / Lei, J. / Pan, X. / Huang, X. / Zhao, Y.
History
DepositionMar 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,8018
Polymers59,7242
Non-polymers1,0776
Water9,764542
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4014
Polymers29,8621
Non-polymers5393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4014
Polymers29,8621
Non-polymers5393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.230, 48.395, 66.213
Angle α, β, γ (deg.)76.290, 75.380, 69.560
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-lactamase / / Penicillinase


Mass: 29861.859 Da / Num. of mol.: 2 / Mutation: E166Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: penP, blaP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00808, beta-lactamase
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH8.0, 25% PEG 3350, 0.2M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979228 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979228 Å / Relative weight: 1
ReflectionResolution: 1.5→63.2 Å / Num. obs: 72109 / % possible obs: 93.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.056 / Χ2: 1.643 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.5-1.531.80.31531171.022182.2
1.53-1.551.80.29832771.111185.4
1.55-1.581.80.28734681.15189.9
1.58-1.621.90.27335321.15191.8
1.62-1.651.90.25236011.248193.7
1.65-1.691.90.2536351.192194.4
1.69-1.7320.23236811.347194.8
1.73-1.7820.19335641.281194.7
1.78-1.8320.16936681.424194.9
1.83-1.8920.13536641.512195.3
1.89-1.9620.11136861.607195.6
1.96-2.0420.09336741.728195.5
2.04-2.1320.07736781.79195.7
2.13-2.2420.06536731.876196.2
2.24-2.3820.05937181.951196.1
2.38-2.5620.05137022196.2
2.56-2.8220.04936662.219196.3
2.82-3.2320.04137042.177195.9
3.23-4.0720.03436472.315195
4.07-5020.03237542.187197.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLM

4blm


Resolution: 1.5→63.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.086
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 3633 5 %RANDOM
Rwork0.1672 ---
obs0.1692 68457 93.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.27 Å2 / Biso mean: 19.568 Å2 / Biso min: 9.45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.5→63.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 68 542 4649
Biso mean--47.19 31.72 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024308
X-RAY DIFFRACTIONr_bond_other_d00.024152
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9945845
X-RAY DIFFRACTIONr_angle_other_deg3.52139676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36124.925201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9215788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4031533
X-RAY DIFFRACTIONr_chiral_restr0.1140.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024689
X-RAY DIFFRACTIONr_gen_planes_other0.010.02808
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 233 -
Rwork0.295 4436 -
all-4669 -
obs--81.85 %

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