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- PDB-5zg6: Crystal structure of beta-lactamase PenP mutant-E166Y in complex ... -

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Basic information

Entry
Database: PDB / ID: 5zg6
TitleCrystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "post-acylation" intermediate
ComponentsBeta-lactamase
KeywordsHYDROLASE / class A beta-lactamase / antibiotic resistance
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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: 2 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,4054
Polymers59,7242
Non-polymers6812
Water1,910106
1
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
2
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
Unit cell
Length a, b, c (Å)43.292, 46.459, 65.981
Angle α, β, γ (deg.)77.43, 75.53, 69.34
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.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH8.0, 25% PEG 3350, 0.4M 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: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→63.2 Å / Num. obs: 29472 / % possible obs: 94 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.073 / Rrim(I) all: 0.135 / Χ2: 1.92 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.032.80.31313070.8640.2130.3811.49883.9
2.03-2.073.10.28914230.9110.1910.3481.4790.9
2.07-2.113.10.2614540.9070.170.3121.44992.2
2.11-2.153.20.24814260.9410.1610.2971.45291.9
2.15-2.23.20.21414690.9440.1370.2551.53392
2.2-2.253.30.21314410.9470.1370.2541.57192
2.25-2.313.30.19614510.9530.1240.2331.54192.4
2.31-2.373.40.18614440.9590.1160.221.58993.3
2.37-2.443.40.17514840.970.110.2071.66493.6
2.44-2.523.40.16314480.9690.1030.1941.69793.9
2.52-2.613.40.1515000.9740.0950.1781.71694.8
2.61-2.713.40.14515060.9780.0920.1731.72495.3
2.71-2.843.40.1414820.980.0880.1661.8195.2
2.84-2.993.40.12315100.9790.0770.1461.87696.2
2.99-3.173.50.11115010.9820.070.1312.06996.2
3.17-3.423.50.08915300.9860.0560.1062.29197
3.42-3.763.50.08115000.9860.0510.0962.76196.3
3.76-4.313.40.07615510.9890.0490.0912.75597.5
4.31-5.433.30.07415080.9890.0490.0892.91197.1
5.43-63.23.10.06715370.9920.0460.0822.6197.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLM

4blm


Resolution: 2→43.06 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25845 1486 5.1 %RANDOM
Rwork0.20819 ---
obs0.21075 27895 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 44 106 4162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134114
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173936
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.6575554
X-RAY DIFFRACTIONr_angle_other_deg2.3931.599130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5545502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33422.5224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26815740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8821530
X-RAY DIFFRACTIONr_chiral_restr0.0760.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024560
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02810
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_it1.3461.6962038
X-RAY DIFFRACTIONr_mcbond_other1.3461.6952037
X-RAY DIFFRACTIONr_mcangle_it2.1632.532530
X-RAY DIFFRACTIONr_mcangle_other2.1632.5322531
X-RAY DIFFRACTIONr_scbond_it1.6741.9252076
X-RAY DIFFRACTIONr_scbond_other1.6741.9252077
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.752.8093025
X-RAY DIFFRACTIONr_long_range_B_refined4.38919.8514506
X-RAY DIFFRACTIONr_long_range_B_other4.38519.8494501
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 97 -
Rwork0.232 1999 -
obs--90.31 %

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