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- PDB-8eo6: Crystal structure of metagenomic class A beta-lactamase precursor... -

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Basic information

Entry
Database: PDB / ID: 8eo6
TitleCrystal structure of metagenomic class A beta-lactamase precursor LRA-5 in complex with ceftazidime at 2.35 Angstrom resolution
ComponentsLRA-5
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase precursor / environmental resistome / soil metagenome / ceftazidime / oxyimino-cephalosporin
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 / ACYLATED CEFTAZIDIME / LRA-5
Function and homology information
Biological speciesuncultured soil bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,8944
Polymers61,9552
Non-polymers9392
Water75742
1
A: LRA-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4472
Polymers30,9771
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LRA-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4472
Polymers30,9771
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.080, 162.110, 70.270
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 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-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.41 Å3/Da / Density % sol: 64 % / Description: long bars
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: 1.6 M sodium formate

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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 prefocusing mirror and a Kirkpatrick-Baez pair of focusing 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: 2.35→43.66 Å / Num. obs: 36200 / % possible obs: 99.7 % / Redundancy: 13.4 % / CC1/2: 0.997 / Rrim(I) all: 0.283 / Net I/σ(I): 11.78
Reflection shellResolution: 2.35→2.49 Å / Redundancy: 12.72 % / Mean I/σ(I) obs: 1.62 / Num. unique obs: 5654 / CC1/2: 0.495 / Rrim(I) all: 2.33 / % possible all: 98.1

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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: 2.35→43.66 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 1806 5 %
Rwork0.1958 --
obs0.1968 36122 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 2.35→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 62 42 4120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.036
X-RAY DIFFRACTIONf_dihedral_angle_d8.217586
X-RAY DIFFRACTIONf_chiral_restr0.05684
X-RAY DIFFRACTIONf_plane_restr0.016728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.35141340.32212566X-RAY DIFFRACTION99
2.41-2.480.31821370.28382603X-RAY DIFFRACTION100
2.48-2.560.25951380.24912609X-RAY DIFFRACTION100
2.56-2.650.29521360.23892595X-RAY DIFFRACTION100
2.65-2.760.27281370.23162600X-RAY DIFFRACTION100
2.76-2.890.27421370.23922610X-RAY DIFFRACTION100
2.89-3.040.27611380.23372619X-RAY DIFFRACTION100
3.04-3.230.21361380.21162623X-RAY DIFFRACTION100
3.23-3.480.22381400.1952644X-RAY DIFFRACTION100
3.48-3.830.21721390.17842644X-RAY DIFFRACTION100
3.83-4.380.17321410.14822678X-RAY DIFFRACTION100
4.38-5.520.16021410.15852695X-RAY DIFFRACTION100
5.52-43.660.17961500.17972830X-RAY DIFFRACTION100

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