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- PDB-3if6: Crystal structure of OXA-46 beta-lactamase from P. aeruginosa -

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Basic information

Entry
Database: PDB / ID: 3if6
TitleCrystal structure of OXA-46 beta-lactamase from P. aeruginosa
Components(OXA-46 oxacillinase) x 3
KeywordsHYDROLASE / serine beta-lactamase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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
L(+)-TARTARIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDocquier, J.D. / Benvenuti, M. / Calderone, V. / Giuliani, F. / Kapetis, D. / De Luca, F. / Rossolini, G.M. / Mangani, S.
Citation
Journal: Antimicrob.Agents Chemother. / Year: 2010
Title: Crystal structure of the narrow-spectrum OXA-46 class D beta-lactamase: relationship between active-site lysine carbamylation and inhibition by polycarboxylates
Authors: Docquier, J.D. / Benvenuti, M. / Calderone, V. / Giuliani, F. / Kapetis, D. / De Luca, F. / Rossolini, G.M. / Mangani, S.
#1: Journal: Antimicrob.Agents Chemother. / Year: 2005
Title: OXA-46, a new class D beta-lactamase of narrow substrate specificity encoded by a blaVIM-1-containing integron from a Pseudomonas aeruginosa clinical isolate
Authors: Giuliani, F. / Docquier, J.D. / Riccio, M.L. / Pagani, L. / Rossolini, G.M.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OXA-46 oxacillinase
B: OXA-46 oxacillinase
C: OXA-46 oxacillinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,33312
Polymers93,3783
Non-polymers9559
Water7,170398
1
A: OXA-46 oxacillinase
hetero molecules

A: OXA-46 oxacillinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8298
Polymers62,2812
Non-polymers5486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
2
B: OXA-46 oxacillinase
C: OXA-46 oxacillinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9188
Polymers62,2382
Non-polymers6816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.838, 123.838, 327.915
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein OXA-46 oxacillinase / OXA-like protein


Mass: 31140.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PPV-97 / Plasmid: peT-9a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8GRH0
#2: Protein OXA-46 oxacillinase / OXA-like protein


Mass: 31097.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PPV-97 / Plasmid: peT-9a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8GRH0
#3: Protein OXA-46 oxacillinase / OXA-like protein


Mass: 31140.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PPV-97 / Plasmid: peT-9a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8GRH0

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Non-polymers , 4 types, 407 molecules

#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1M Na,K L-tartrate tetrahydrate, 50mM Hepes, 2-4%(v/v) PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.92 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 28, 2005
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→56.5 Å / Num. all: 48568 / Num. obs: 48227 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.2 / Redundancy: 8.8 % / Biso Wilson estimate: 42.418 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.78 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.2 / Num. unique all: 756 / Rsym value: 0.61 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.4→31.4 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.322 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.438 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28519 3404 9.1 %RANDOM
Rwork0.21115 ---
all0.21793 34100 --
obs0.21793 34100 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.818 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.303 Å0.438 Å
Refinement stepCycle: LAST / Resolution: 2.4→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 63 398 6286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226034
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9318149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3555695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87922.812320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8031562
X-RAY DIFFRACTIONr_chiral_restr0.1130.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024668
X-RAY DIFFRACTIONr_nbd_refined0.2230.22988
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2415
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.211
X-RAY DIFFRACTIONr_mcbond_it0.811.53598
X-RAY DIFFRACTIONr_mcangle_it1.42225620
X-RAY DIFFRACTIONr_scbond_it1.99532855
X-RAY DIFFRACTIONr_scangle_it3.0514.52529
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 265 -
Rwork0.26 2497 -
obs-2497 100 %

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