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- PDB-4gn2: Crystal Structure of OXA-45, a Class D beta-lactamase with extend... -

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Basic information

Entry
Database: PDB / ID: 4gn2
TitleCrystal Structure of OXA-45, a Class D beta-lactamase with extended spectrum activity
ComponentsOxacillinase
KeywordsHYDROLASE / beta-lactamase / antibiotic resistance / lysine carbamylation / alpha/beta
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase activity / beta-lactamase / plasma membrane
Similarity search - Function
: / 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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsMartin, J.D. / Xiong, X.L. / Catto, L.E. / Toleman, M.A. / Walsh, T.R. / Clarke, A.R. / Spencer, J.
CitationJournal: To be Published
Title: Structural and Kinetic Characterization of OXA-45, a Class D beta-Lactamase with Extended Spectrum activity
Authors: Martin, J.D. / Xiong, X.L. / Catto, L.E. / Toleman, M.A. / Walsh, T.R. / Clarke, A.R. / Spencer, J.
History
DepositionAug 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ref_seq_dif
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_ref_seq_dif.details
Revision 1.2Dec 6, 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

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Assembly

Deposited unit
A: Oxacillinase


Theoretical massNumber of molelcules
Total (without water)25,9561
Polymers25,9561
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.169, 47.488, 108.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Oxacillinase / Oxacillinase Oxa45


Mass: 25956.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: 07-406 / Gene: blaoxa45, oxa45 / Plasmid: pK18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q7WZC7, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 22% PEG 4K 10% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Feb 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→30 Å / Num. obs: 16275 / % possible obs: 100 % / Rmerge(I) obs: 0.141 / Χ2: 1.026 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.01-2.080.43515910.943199.9
2.08-2.170.36115960.9341100
2.17-2.260.3216120.9171100
2.26-2.380.28415850.9291100
2.38-2.530.24716030.9761100
2.53-2.730.20416011.0181100
2.73-30.16316441.0881100
3-3.440.11216261.1951100
3.44-4.330.08116521.1381100
4.33-300.06717651.081199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M6K

1m6k


Resolution: 2.01→27.226 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1853 / WRfactor Rwork: 0.1461 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8564 / SU B: 8.579 / SU ML: 0.108 / SU Rfree: 0.1638 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 818 5 %RANDOM
Rwork0.166 ---
obs0.1685 16228 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.82 Å2 / Biso mean: 18.1965 Å2 / Biso min: 8.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å20 Å2
2---0.37 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.01→27.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 0 281 2112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191889
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9432561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5985241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66323.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53715290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7211511
X-RAY DIFFRACTIONr_chiral_restr0.0740.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211469
X-RAY DIFFRACTIONr_rigid_bond_restr2.67431889
X-RAY DIFFRACTIONr_sphericity_free23.879573
X-RAY DIFFRACTIONr_sphericity_bonded5.83152045
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 73 -
Rwork0.182 995 -
all-1068 -
obs--99.81 %

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