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- PDB-4hbt: Crystal structure of native CTX-M-15 extended-spectrum beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 4hbt
TitleCrystal structure of native CTX-M-15 extended-spectrum beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / Hydrolysis of beta-lactams / Antibiotic resistance
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsDocquier, J.D. / Benvenuti, M. / Bruneau, J.M. / Rossolini, G.M. / Miossec, C. / Black, M.T. / Mangani, S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Structural insight into potent broad-spectrum inhibition with reversible recyclization mechanism: avibactam in complex with CTX-M-15 and Pseudomonas aeruginosa AmpC beta-lactamases
Authors: Lahiri, S.D. / Mangani, S. / Durand-Reville, T. / Benvenuti, M. / De Luca, F. / Sanyal, G. / Docquier, J.D.
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Dec 4, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,15115
Polymers28,1391
Non-polymers1,01214
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.698, 45.720, 117.086
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 / Beta-lactamase CTX-M / Beta-lactamase CTX-M-15 / Beta-lactamase bla-CTX-M-15 / BlaCTX-M-15 / CTX-M- ...Beta-lactamase CTX-M / Beta-lactamase CTX-M-15 / Beta-lactamase bla-CTX-M-15 / BlaCTX-M-15 / CTX-M-15 / CTX-M-15 beta-lactamase / CTX-M-15 extended-spectrum beta-lactamase / CTX-m-3-like beta-lactamase / Extended-spectrum beta-lactamase CTX-M-15


Mass: 28138.826 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaUOE-1, bla, bla CTX-M-15, blaCTX-M-15, blaCTX-M15, CTX-M-15
Production host: Escherichia coli (E. coli) / References: UniProt: Q9EXV5, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-HCl, 2.2-2.4M ammonium sulfate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2009
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.1→29.273 Å / Num. all: 97968 / Num. obs: 97955 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.1→1.16 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IYS

1iys


Resolution: 1.1→29.27 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.575 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13644 4884 5 %RANDOM
Rwork0.11691 ---
obs0.11789 92994 99.69 %-
all-98258 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.1→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 58 239 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022101
X-RAY DIFFRACTIONr_bond_other_d0.0010.021441
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.9852849
X-RAY DIFFRACTIONr_angle_other_deg1.02833527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73424.31888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44615363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2581518
X-RAY DIFFRACTIONr_chiral_restr0.1180.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr6.38633542
X-RAY DIFFRACTIONr_sphericity_free22.533563
X-RAY DIFFRACTIONr_sphericity_bonded9.01953695
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 331 -
Rwork0.171 6381 -
obs--98.87 %

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