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- PDB-5zft: Crystal structure of beta-lactamase PenP mutant-E166Y in complex ... -

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Basic information

Entry
Database: PDB / ID: 5zft
TitleCrystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "pre-deacylation" intermediate
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
Chem-CED / Beta-lactamase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 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 7, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,4054
Polymers59,7242
Non-polymers6812
Water2,378132
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2022
Polymers29,8621
Non-polymers3401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2022
Polymers29,8621
Non-polymers3401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.240, 45.880, 66.090
Angle α, β, γ (deg.)77.63, 75.51, 69.27
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-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.: 132 / 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: 37.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH8.0, 25% PEG 33500, 4M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→42.49 Å / Num. obs: 32004 / % possible obs: 92.8 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.03 / Rrim(I) all: 0.059 / Net I/σ(I): 18.3
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 8.4 / CC1/2: 0.981 / Rpim(I) all: 0.079 / Rrim(I) all: 0.156 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLM

4blm


Resolution: 1.93→35.1 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21759 1624 5.1 %RANDOM
Rwork0.17751 ---
obs0.17952 30373 92.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.767 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.93→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 44 132 4212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134306
X-RAY DIFFRACTIONr_bond_other_d0.0340.0174120
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.6575853
X-RAY DIFFRACTIONr_angle_other_deg2.3521.5919607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8422.757243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02615796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3941532
X-RAY DIFFRACTIONr_chiral_restr0.0890.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024834
X-RAY DIFFRACTIONr_gen_planes_other0.010.02850
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_it1.1621.3022106
X-RAY DIFFRACTIONr_mcbond_other1.1531.32105
X-RAY DIFFRACTIONr_mcangle_it1.8541.9412626
X-RAY DIFFRACTIONr_mcangle_other1.8541.9432627
X-RAY DIFFRACTIONr_scbond_it1.8961.6082200
X-RAY DIFFRACTIONr_scbond_other1.8961.6092201
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1012.313202
X-RAY DIFFRACTIONr_long_range_B_refined4.63215.544778
X-RAY DIFFRACTIONr_long_range_B_other4.6315.5424777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.926→1.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 120 -
Rwork0.194 2041 -
obs--84.65 %

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