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- PDB-4f94: Structure of the Class D Beta-Lactamase OXA-24 K84D in Acyl-Enzym... -

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Basic information

Entry
Database: PDB / ID: 4f94
TitleStructure of the Class D Beta-Lactamase OXA-24 K84D in Acyl-Enzyme Complex with Oxacillin
ComponentsBeta-lactamase
KeywordsHydrolase/Antibiotic / Carbapenemase / Hydrolase-Antibiotic complex
Function / homology
Function and homology information


penicillin binding / beta-lactamase activity
Similarity search - Function
Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1S6 / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJune, C.M. / Vallier, B.C. / Bonomo, R.A. / Leonard, D.A. / Powers, R.A.
CitationJournal: To be Published
Title: Structure of the Class D Beta-Lactamase OXA-24 K84D in Acyl-Enzyme Complex with Oxacillin
Authors: June, C.M. / Vallier, B.C. / Bonomo, R.A. / Leonard, D.A. / Powers, R.A.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Non-polymer description
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _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)28,4486
Polymers27,6611
Non-polymers7885
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.334, 102.334, 87.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

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Components

#1: Protein Beta-lactamase / Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / ...Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing oxacillinase / Carbapenemase OXA-24 / Class D beta-lactamase OXA-40 / OXA-24 class D beta-lactamase / Oxa40


Mass: 27660.760 Da / Num. of mol.: 1 / Fragment: UNP residues 32-275 / Mutation: K84D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: bla, bla-OXA-40, blaOXA-24, blaOXA-33, blaOXA-40, oxa-24, oxa40
Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RLA6, beta-lactamase
#2: Chemical ChemComp-1S6 / (2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid / Oxacillin, bound form


Mass: 403.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 4.14 Å3/Da / Density % sol: 70.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1% (v/v) PEG 400, 1.0 M Ammonium Sulfate, 0.05 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 18309 / Num. obs: 18309 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3.67 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2JC7

2jc7


Resolution: 2.4→30.37 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.89 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21402 937 5.2 %RANDOM
Rwork0.17788 ---
obs0.17975 17254 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.724 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2---1.47 Å20 Å2
3---2.94 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 48 110 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192057
X-RAY DIFFRACTIONr_bond_other_d0.0010.021981
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.9792790
X-RAY DIFFRACTIONr_angle_other_deg0.88734563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26825.54392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88115379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.004158
X-RAY DIFFRACTIONr_chiral_restr0.220.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
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_it1.181.51228
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17321982
X-RAY DIFFRACTIONr_scbond_it3.4733836
X-RAY DIFFRACTIONr_scangle_it5.4874.5813
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 80 -
Rwork0.181 1267 -
obs--99.04 %

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