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- PDB-1k4e: CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASES OXA-10 DETERMINE... -

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Basic information

Entry
Database: PDB / ID: 1k4e
TitleCRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASES OXA-10 DETERMINED BY MAD PHASING WITH SELENOMETHIONINE
ComponentsBeta-lactamase PSE-2
KeywordsHYDROLASE / beta-lactamase / MAD phasing / selenomethionine / carbamylated lysine
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / plasma membrane
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
Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKerff, F. / Fonze, E. / Bouillene, F. / Frere, J.M. / Charlier, P.
CitationJournal: To be Published
Title: STRUCTURE OF CLASS D BETA-LACTAMASE OXA-2
Authors: Kerff, F. / Fonze, E. / Bouillene, F. / Frere, J.M. / Charlier, P.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _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 PSE-2
B: Beta-lactamase PSE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2685
Polymers55,9802
Non-polymers2883
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-54 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.562, 102.273, 126.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a dimer in the asymmetric unit formed by chains A and B

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Components

#1: Protein Beta-lactamase PSE-2 / Beta lactamase OXA-10


Mass: 27990.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: plasmid pMON234 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulfate, bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9791, 0.9793, 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 7, 2000
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.91841
ReflectionResolution: 1.8→27.2 Å / Num. all: 55652 / Num. obs: 55652 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 10.4 Å2 / Rsym value: 0.068 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 0.6 / Rsym value: 0.686 / % possible all: 75.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→19.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2063465.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2041 5 %RANDOM
Rwork0.201 ---
obs0.201 40722 93.8 %-
all-40752 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3522 Å2 / ksol: 0.356966 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å20 Å20 Å2
2--1.05 Å20 Å2
3----4.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 15 345 4250
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.245 152 4.4 %
Rwork0.209 3340 -
obs--81.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_PSE.PARAMPROTEIN-PSE.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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