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- PDB-8eo5: Crystal structure of the class A beta-lactamase precursor LRA-5 f... -

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Basic information

Entry
Database: PDB / ID: 8eo5
TitleCrystal structure of the class A beta-lactamase precursor LRA-5 from an Alaskan soil metagenome at 1.8 Angstrom resolution
ComponentsLRA-5
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase precursor / environmental resistome / soil metagenome
Function / homologyBeta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / beta-lactam antibiotic catabolic process / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like / beta-lactamase activity / response to antibiotic / LRA-5
Function and homology information
Biological speciesuncultured soil bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LRA-5
B: LRA-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0773
Polymers61,9552
Non-polymers1221
Water4,882271
1
A: LRA-5


Theoretical massNumber of molelcules
Total (without water)30,9771
Polymers30,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LRA-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1002
Polymers30,9771
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.270, 162.620, 71.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-514-

HOH

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Components

#1: Protein LRA-5


Mass: 30977.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured soil bacterium (environmental samples)
Gene: blaLRA-5, AKSOIL_0013 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5L5W7
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.47 Å3/Da / Density % sol: 65 % / Description: long bars
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 13% PEG 20,000 + 0.1M Tris pH 8.2 + 0.1 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2021
Details: convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Cryogenically cooled channel cut crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 1.8→48.94 Å / Num. obs: 80573 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.99 / Rrim(I) all: 0.131 / Net I/σ(I): 15.57
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 13.77 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 12790 / CC1/2: 0.556 / Rrim(I) all: 2.172 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.2_4158phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+25 / Resolution: 1.8→48.94 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 4027 5 %
Rwork0.189 --
obs0.1903 80557 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 8 271 4314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174109
X-RAY DIFFRACTIONf_angle_d1.4745586
X-RAY DIFFRACTIONf_dihedral_angle_d9.38584
X-RAY DIFFRACTIONf_chiral_restr0.101683
X-RAY DIFFRACTIONf_plane_restr0.009721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.38711340.35782538X-RAY DIFFRACTION97
1.82-1.840.28141370.28962608X-RAY DIFFRACTION100
1.84-1.870.30111380.2782618X-RAY DIFFRACTION100
1.87-1.890.30281350.26782571X-RAY DIFFRACTION100
1.89-1.920.27311390.26682629X-RAY DIFFRACTION100
1.92-1.940.27611380.25352625X-RAY DIFFRACTION100
1.94-1.970.24071370.2362603X-RAY DIFFRACTION100
1.97-20.24131370.2182610X-RAY DIFFRACTION100
2-2.040.28921370.22152599X-RAY DIFFRACTION100
2.04-2.070.22341380.21372620X-RAY DIFFRACTION100
2.07-2.110.26271390.20132638X-RAY DIFFRACTION100
2.11-2.150.21941370.19972600X-RAY DIFFRACTION100
2.15-2.190.22241370.1942616X-RAY DIFFRACTION100
2.19-2.240.21671390.1892627X-RAY DIFFRACTION100
2.24-2.290.22891390.19382640X-RAY DIFFRACTION100
2.29-2.350.24241370.18982614X-RAY DIFFRACTION100
2.35-2.410.25041380.19572615X-RAY DIFFRACTION100
2.41-2.480.19261390.19372638X-RAY DIFFRACTION100
2.48-2.560.2211400.18692668X-RAY DIFFRACTION100
2.56-2.660.21651370.19142612X-RAY DIFFRACTION100
2.66-2.760.21491390.19272634X-RAY DIFFRACTION100
2.76-2.890.20751390.19292642X-RAY DIFFRACTION100
2.89-3.040.23381400.19322652X-RAY DIFFRACTION100
3.04-3.230.21941420.20292694X-RAY DIFFRACTION100
3.23-3.480.22841380.19722638X-RAY DIFFRACTION100
3.48-3.830.20041420.18032681X-RAY DIFFRACTION100
3.83-4.390.18191420.1542703X-RAY DIFFRACTION100
4.39-5.520.20931440.16062733X-RAY DIFFRACTION100
5.52-48.940.16831490.16392864X-RAY DIFFRACTION100

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