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- PDB-4s2p: Crystal structure of unbound OXA-48 -

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Basic information

Entry
Database: PDB / ID: 4s2p
TitleCrystal structure of unbound OXA-48
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKing, D.T. / Strynadka, N.C.J.
CitationJournal: ACS Infect Dis / Year: 2015
Title: Molecular Mechanism of Avibactam-Mediated beta-Lactamase Inhibition.
Authors: King, D.T. / King, A.M. / Lal, S.M. / Wright, G.D. / Strynadka, N.C.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)60,8792
Polymers60,8792
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)30,4401
Polymers30,4401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)30,4401
Polymers30,4401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.410, 102.870, 124.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

21A-476-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A25 - 264
2010B25 - 264
DetailsThis protein behaves as a dimer in solution

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Components

#1: Protein Beta-lactamase


Mass: 30439.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, FP68_27275, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM tris pH 7.5, 0.1M ammonium chloride, 40% MPD, 5% PEG 8K, 100 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→41.6 Å / Num. all: 62413 / Num. obs: 62226 / % possible obs: 99.7 %
Reflection shellResolution: 1.7→1.73 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.8.0071refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.669 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22601 3151 5.1 %RANDOM
Rwork0.19188 ---
obs0.19358 59033 99.58 %-
all-59210 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.524 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--0.79 Å20 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3951 0 0 342 4293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194064
X-RAY DIFFRACTIONr_bond_other_d0.0030.023813
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9165505
X-RAY DIFFRACTIONr_angle_other_deg0.80238743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44724.563206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91815704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8171522
X-RAY DIFFRACTIONr_chiral_restr0.2140.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024667
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021019
X-RAY DIFFRACTIONr_mcbond_it2.8362.4881945
X-RAY DIFFRACTIONr_mcbond_other2.8372.4881944
X-RAY DIFFRACTIONr_mcangle_it3.7263.7292433
X-RAY DIFFRACTIONr_mcangle_other3.7253.732434
X-RAY DIFFRACTIONr_scbond_it3.9072.8452119
X-RAY DIFFRACTIONr_scbond_other3.9022.8452119
X-RAY DIFFRACTIONr_scangle_other5.64.1313072
X-RAY DIFFRACTIONr_long_range_B_refined7.00321.6415391
X-RAY DIFFRACTIONr_long_range_B_other6.95821.2985213
Refine LS restraints NCS

Ens-ID: 1 / Number: 15864 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 238 -
Rwork0.287 4355 -
obs--99.85 %

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