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- PDB-8eo7: Crystal structure of metagenomic beta-lactamase LRA-5 Y69Q/V166E ... -

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Basic information

Entry
Database: PDB / ID: 8eo7
TitleCrystal structure of metagenomic beta-lactamase LRA-5 Y69Q/V166E mutant at 2.15 Angstrom resolution
Componentsbeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase precursor / environmental resistome / soil metagenome / mutant
Function / homologyBeta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / beta-lactam antibiotic catabolic process / Beta-lactamase/transpeptidase-like / beta-lactamase activity / beta-lactamase / response to antibiotic / beta-lactamase
Function and homology information
Biological speciesuncultured soil bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPower, P. / D'Amico Gonzalez, G. / Centron, D. / Gutkind, G. / Handelsman, J. / Klinke, S.
Funding support Argentina, 2items
OrganizationGrant numberCountry
National Scientific and Technical Research Council (CONICET)11220200100191CO Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2018 01550 Argentina
CitationJournal: to be published
Title: Playing beta-Lactamase Evolution: Metagenomic Class A beta-Lactamase LRA-5 is an Inactive Enzyme Capable of Rendering an Active beta-Lactamase by Introduction of Y69Q and V166E Substitutions
Authors: D'Amico Gonzalez, G. / Handelsman, J. / Centron, D. / Gutkind, G. / Klinke, S. / Power, P.
History
DepositionOct 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-lactamase
B: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)61,9452
Polymers61,9452
Non-polymers00
Water1,838102
1
A: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)30,9721
Polymers30,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)30,9721
Polymers30,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.861, 162.236, 70.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein beta-lactamase /


Mass: 30972.346 Da / Num. of mol.: 2 / Mutation: Y100Q, V199E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured soil bacterium (environmental samples)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5L5W7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.41 Å3/Da / Density % sol: 64 % / Description: long bars
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: 1.50 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 29, 2021 / Details: Horizontally and vertically focusing mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→48.58 Å / Num. obs: 46812 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.07 / Rrim(I) all: 0.26 / Net I/σ(I): 7.3
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.721 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4010 / CC1/2: 0.687 / Rpim(I) all: 0.75 / Rrim(I) all: 2.823 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+25 / Resolution: 2.15→40.56 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 2189 5.02 %
Rwork0.2253 --
obs0.2264 43641 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 0 102 3858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053800
X-RAY DIFFRACTIONf_angle_d0.9645153
X-RAY DIFFRACTIONf_dihedral_angle_d9.551531
X-RAY DIFFRACTIONf_chiral_restr0.05642
X-RAY DIFFRACTIONf_plane_restr0.005663
LS refinement shellResolution: 2.15→2.17 Å
RfactorNum. reflection% reflection
Rfree0.4323 92 -
Rwork0.3956 1413 -
obs--100 %

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