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- PDB-3hbr: Crystal structure of OXA-48 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 3hbr
TitleCrystal structure of OXA-48 beta-lactamase
ComponentsOXA-48
KeywordsHYDROLASE / CLASS D BETA-LACTAMASE / OXA-48 / ANTIBIOTIC / DIMER
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / 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-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCalderone, V. / Mangani, S. / Benvenuti, M. / Rossolini, G.M. / Docquier, J.D.
Citation
Journal: Chem.Biol. / Year: 2009
Title: Crystal structure of the OXA-48 beta-lactamase reveals mechanistic diversity among class D carbapenemases.
Authors: Docquier, J.D. / Calderone, V. / De Luca, F. / Benvenuti, M. / Giuliani, F. / Bellucci, L. / Tafi, A. / Nordmann, P. / Botta, M. / Rossolini, G.M. / Mangani, S.
#1: Journal: J.Am.Chem.Soc. / Year: 2000
Title: The first structural and mechanistic insights for class D beta-lactamases: evidence for a novel catalytic process for turnover of beta-lactam antibiotics
Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Tranier, S. / Ishiwata, A. / Kotra, L.P. / Samama, J.P. / Mobashery, S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases
Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Samama, J.P. / Mobashery, S.
History
DepositionMay 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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 1.3Nov 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-48
B: OXA-48
C: OXA-48
D: OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0078
Polymers121,7594
Non-polymers2484
Water13,727762
1
A: OXA-48
B: OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0665
Polymers60,8792
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: OXA-48
D: OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9423
Polymers60,8792
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5022
Polymers30,4401
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5643
Polymers30,4401
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5022
Polymers30,4401
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: OXA-48


Theoretical massNumber of molelcules
Total (without water)30,4401
Polymers30,4401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.701, 107.185, 80.787
Angle α, β, γ (deg.)90.00, 111.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
OXA-48


Mass: 30439.725 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 11978 / Gene: bla OXA-48 / Plasmid: pet9a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 10% PEG 4000, 8% 1-BUTANOL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2005 / Details: mirrors
RadiationMonochromator: Diamond (111), Laue geometry, 150 microns thin
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→30.514 Å / Num. all: 71756 / Num. obs: 71756 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.1004 / Net I/σ(I): 5.3
Reflection shellResolution: 1.9→1.949 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.176 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K4F

1k4f


Resolution: 1.9→30.51 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.828 / SU B: 4.719 / SU ML: 0.143 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28618 7101 9 %RANDOM
Rwork0.21691 ---
obs0.22315 71756 100 %-
all-71756 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.906 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7857 0 16 762 8635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.91510897
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5075953
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72624.532417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.962151409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7331546
X-RAY DIFFRACTIONr_chiral_restr0.1150.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026166
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.24496
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25478
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2718
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8551.54927
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33527672
X-RAY DIFFRACTIONr_scbond_it2.10633713
X-RAY DIFFRACTIONr_scangle_it2.8994.53225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 522 -
Rwork0.235 5316 -
obs--100 %

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