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- PDB-2wgw: Crystal structure of the OXA-10 V117T mutant at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 2wgw
TitleCrystal structure of the OXA-10 V117T mutant at pH 8.0
Components(BETA-LACTAMASE OXA-10) x 2
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / TRANSPOSABLE
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVercheval, L. / Kerff, F. / Bauvois, C. / Sauvage, E. / Guiet, R. / Charlier, P. / Galleni, M.
CitationJournal: Biochem.J. / Year: 2010
Title: Three Factors that Modulate the Activity of Class D Beta-Lactamases and Interfere with the Post-Translational Carboxylation of Lys70.
Authors: Vercheval, L. / Bauvois, C. / Di Paolo, A. / Borel, F. / Ferrer, J.L. / Sauvage, E. / Matagne, A. / Frere, J.M. / Charlier, P. / Galleni, M. / Kerff, F.
History
DepositionApr 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE OXA-10
B: BETA-LACTAMASE OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,68515
Polymers55,4722
Non-polymers1,21313
Water9,314517
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-62.5 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.650, 96.620, 126.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA-LACTAMASE OXA-10 / BETA-LACTAMASE PSE-2


Mass: 27757.514 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET 22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase
#2: Protein BETA-LACTAMASE OXA-10 / BETA-LACTAMASE PSE-2


Mass: 27714.512 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET 22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 117 TO THR ENGINEERED RESIDUE IN CHAIN B, VAL 117 TO THR
Sequence detailsLYS A 70 AND KCX (LYSINE NZ-CARBOXYLIC ACID) A 70 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. IN ...LYS A 70 AND KCX (LYSINE NZ-CARBOXYLIC ACID) A 70 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. IN CHAIN A, THE STRUCTURE WAS MODELLED AS A MIXTURE OF CARBONATED AND UNCARBONATED FORM.

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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: 2.29 Å3/Da / Density % sol: 45.96 % / Description: NONE
Crystal growpH: 8 / Details: 1.8 M AS BUFFER HEPES 0.1 M PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979724
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979724 Å / Relative weight: 1
ReflectionResolution: 1.8→48.62 Å / Num. obs: 55385 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 13.45 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.7 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4F

1k4f


Resolution: 1.8→38.52 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.903 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2808 5.1 %RANDOM
Rwork0.149 ---
obs0.151 52492 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.418 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 74 517 4493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224181
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9585661
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1275525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06525.169178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41715746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3191516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023105
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22137
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22940
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2386
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1151.52642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6624138
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.49231801
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8184.51523
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.51334443
X-RAY DIFFRACTIONr_sphericity_free4.0733517
X-RAY DIFFRACTIONr_sphericity_bonded2.11634094
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 173 -
Rwork0.154 3494 -
obs--91.33 %

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