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- PDB-1e25: The high resolution structure of PER-1 class A beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 1.0E+25
TitleThe high resolution structure of PER-1 class A beta-lactamase
ComponentsEXTENDED-SPECTRUM BETA-LACTAMASE PER-1
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / CLASS A CEPHALOSPORINASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region
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
Extended-spectrum beta-lactamase PER-1
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsTranier, S. / Bouthors, A.T. / Maveyraud, L. / Guillet, V. / Sougakoff, W. / Samama, J.P.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The High Resolution Crystal Structure for Class a Beta-Lactamase Per-1 Reveals the Bases for its Increase in Breadth of Activity
Authors: Tranier, S. / Bouthors, A.T. / Maveyraud, L. / Guillet, V. / Sougakoff, W. / Samama, J.P.
History
DepositionMay 17, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: EXTENDED-SPECTRUM BETA-LACTAMASE PER-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0422
Polymers30,9461
Non-polymers961
Water2,756153
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.600, 84.600, 46.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein EXTENDED-SPECTRUM BETA-LACTAMASE PER-1


Mass: 30945.529 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: RNL-1 / Gene: BLAPER-1 / Plasmid: PK19 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P37321, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION GLY239GLN

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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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 4.7
Details: 18% (V/V) SATURATED AMMONIUM SULFATE, 1MM DITHIOTHREITOL, 100 MM SODIUM ACETATE, PH4.7, pH 4.70
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 7.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1drop
30.5 mMdithiothreitol1drop
40.06 %1dropNaN3
518 %(v/v)satammonium sulfate1reservoir
60.1 Msodium acetate1reservoir
71 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→24.18 Å / Num. obs: 25029 / % possible obs: 94.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 11.6 Å2 / Rsym value: 0.052 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.122 / % possible all: 93.7
Reflection
*PLUS
Num. measured all: 66657 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 93.7 % / Rmerge(I) obs: 0.122

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNS0.5phasing
SHARPphasing
CNS0.5refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→19.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1509650.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE 3 C-TERMINAL RESIDUES AND THE FIRST N-TERMINAL RESIDUE WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2533 9.9 %RANDOM
Rwork0.14 ---
obs0.14 25707 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.0192 Å2 / ksol: 0.364363 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2--1.04 Å20 Å2
3----2.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 5 153 2300
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.543
X-RAY DIFFRACTIONc_mcangle_it3.445
X-RAY DIFFRACTIONc_scbond_it6.47
X-RAY DIFFRACTIONc_scangle_it8.8210
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.217 423 9.9 %
Rwork0.185 3835 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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