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- PDB-3zny: Crystal structure of the class A extended-spectrum beta-lactamase... -

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Basic information

Entry
Database: PDB / ID: 3zny
TitleCrystal structure of the class A extended-spectrum beta-lactamase CTX- M-96, a natural D240G mutant derived from CTX-M-12
ComponentsCTX-M-12A ENZYME
KeywordsHYDROLASE / OXYIMINO-CEPHALOSPORINASE / CEFTAZIDIMASE
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 speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPower, P. / Herman, R. / Bouillenne, F. / Ghiglione, B. / Rodriguez, M.M. / Galleni, M. / Gutkind, G. / Charlier, P. / Sauvage, E.
CitationJournal: Biochemistry / Year: 2015
Title: Structural and Kinetic Insights Into the "Ceftazidimase" Behavior of the Extended-Spectrum Beta-Lactamase Ctx-M-96.
Authors: Ghiglione, B. / Rodriguez, M.M. / Herman, R. / Curto, L.M. / Dropa, M. / Bouillenne, F. / Kerff, F. / Galleni, M. / Charlier, P. / Gutkind, G. / Sauvage, E. / Power, P.
History
DepositionFeb 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTX-M-12A ENZYME


Theoretical massNumber of molelcules
Total (without water)28,1261
Polymers28,1261
Non-polymers00
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.569, 45.586, 117.403
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 CTX-M-12A ENZYME / CLASS A BETA-LACTAMASE


Mass: 28125.826 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6ZXB6, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 1.81 Å3/Da / Density % sol: 31.35 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.2→45.59 Å / Num. obs: 75509 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.1
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6.7 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YLP

1ylp


Resolution: 1.2→42.5 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.924 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16658 3787 5 %RANDOM
Rwork0.14041 ---
obs0.14171 71553 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.782 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.2→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 0 362 2312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9712719
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9755264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26624.32181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62415353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1511516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211482
X-RAY DIFFRACTIONr_gen_planes_other
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.47832004
X-RAY DIFFRACTIONr_sphericity_free21.345578
X-RAY DIFFRACTIONr_sphericity_bonded9.17952259
LS refinement shellResolution: 1.196→1.227 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 229 -
Rwork0.226 4328 -
obs--85.77 %

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