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- PDB-3lce: Crystal Structure of Oxa-10 Beta-Lactamase Covalently Bound to Cy... -

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Basic information

Entry
Database: PDB / ID: 3lce
TitleCrystal Structure of Oxa-10 Beta-Lactamase Covalently Bound to Cyclobutanone Beta-Lactam Mimic
ComponentsBeta-lactamase OXA-10
KeywordsHYDROLASE / beta-lactamase / beta-lactamase inhibitor / beta-lactam mimic / cyclobutanone / hemiketal / Antibiotic resistance / Disulfide bond / Plasmid / Transposable element
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / 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
Chem-LCE / PHOSPHATE ION / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / REFMAC rigid body refinement / Resolution: 2 Å
AuthorsGretes, M. / Strynadka, N.C.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Cyclobutanone Analogues of beta-Lactams Revisited: Insights into Conformational Requirements for Inhibition of Serine- and Metallo-beta-Lactamases.
Authors: Johnson, J.W. / Gretes, M. / Goodfellow, V.J. / Marrone, L. / Heynen, M.L. / Strynadka, N.C. / Dmitrienko, G.I.
History
DepositionJan 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Beta-lactamase OXA-10
B: Beta-lactamase OXA-10
C: Beta-lactamase OXA-10
D: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,01419
Polymers110,2694
Non-polymers1,74515
Water16,520917
1
A: Beta-lactamase OXA-10
C: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8698
Polymers55,1352
Non-polymers7346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-18 kcal/mol
Surface area19860 Å2
MethodPISA
2
B: Beta-lactamase OXA-10
D: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,14511
Polymers55,1352
Non-polymers1,0119
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-16 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.700, 82.544, 102.360
Angle α, β, γ (deg.)90.000, 94.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase OXA-10 / Beta-lactamase PSE-2


Mass: 27567.293 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: AH / References: UniProt: P14489, beta-lactamase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-LCE / (1S,3S,4S,5S)-7,7-dichloro-3-methoxy-2-thiabicyclo[3.2.0]heptan-6-one-4-carboxylic acid / (1S,3S,4S,5S)-7,7-dichloro-3-methoxy-6-oxo-2-thiabicyclo[3.2.0]heptane-4-carboxylic acid


Mass: 271.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8Cl2O4S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 917 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4 M sodium potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.917→102.062 Å / Num. all: 84571 / Num. obs: 84571 / % possible obs: 97.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / Num. measured all: 36298 / Num. unique all: 11881 / Rsym value: 0.35 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
REFMAC5.5.0066phasing
RefinementMethod to determine structure: REFMAC rigid body refinement
Starting model: PDB entry 1e4d

1e4d


Resolution: 2→102.06 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.87 / SU B: 3.682 / SU ML: 0.105 / SU R Cruickshank DPI: 0.185 / SU Rfree: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3651 5 %RANDOM
Rwork0.178 ---
obs0.181 73266 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.78 Å2 / Biso mean: 20.045 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0.48 Å2
2---0.12 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→102.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7862 0 106 917 8885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228138
X-RAY DIFFRACTIONr_angle_refined_deg1.781.95911010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66351004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48225.14358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.033151442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7111533
X-RAY DIFFRACTIONr_chiral_restr0.1260.21199
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216053
X-RAY DIFFRACTIONr_mcbond_it0.991.54956
X-RAY DIFFRACTIONr_mcangle_it1.73828003
X-RAY DIFFRACTIONr_scbond_it3.02533182
X-RAY DIFFRACTIONr_scangle_it4.9034.53003
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 268 -
Rwork0.23 5121 -
all-5389 -
obs--99.17 %

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