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- PDB-1g68: PSE-4 CARBENICILLINASE, WILD TYPE -

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Basic information

Entry
Database: PDB / ID: 1g68
TitlePSE-4 CARBENICILLINASE, WILD TYPE
ComponentsBETA-LACTAMASE PSE-4
KeywordsHYDROLASE / class A beta-lactamase / carbenicillinase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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
Beta-lactamase PSE-4
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLim, D. / Sanschagrin, F. / Passmore, L. / De Castro, L. / Levesque, R.C. / Strynadka, N.C.J.
CitationJournal: Biochemistry / Year: 2001
Title: Insights into the molecular basis for the carbenicillinase activity of PSE-4 beta-lactamase from crystallographic and kinetic studies.
Authors: Lim, D. / Sanschagrin, F. / Passmore, L. / De Castro, L. / Levesque, R.C. / Strynadka, N.C.
History
DepositionNov 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE RESIDUE NUMBERING IN NOT SEQUENTIAL. RESIDUES 57 AND 59, 238 AND 240, 252 AND 254 ARE ...SEQUENCE THE RESIDUE NUMBERING IN NOT SEQUENTIAL. RESIDUES 57 AND 59, 238 AND 240, 252 AND 254 ARE COVALENTLY BOUND.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE PSE-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6522
Polymers29,5561
Non-polymers961
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.197, 95.197, 62.793
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-536-

HOH

21A-646-

HOH

31A-648-

HOH

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Components

#1: Protein BETA-LACTAMASE PSE-4 / CARBENICILLINASE 1


Mass: 29556.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PSE4 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 LAMDADE3 / References: UniProt: P16897, 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.: 298 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, MgCl2, MOPS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
350 mMMOPS1reservoir
4100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 28, 1999 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. all: 21494 / Num. obs: 21494 / % possible obs: 99.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 33
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.219 / Num. unique all: 2035 / % possible all: 96.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 208439
Reflection shell
*PLUS
% possible obs: 96.5 % / Mean I/σ(I) obs: 8.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TEM-1 native structure

Resolution: 1.95→24.34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2038344.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1049 4.9 %RANDOM
Rwork0.167 ---
obs0.167 21462 99.3 %-
all-21494 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.96 Å2 / ksol: 0.4186 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2---1.33 Å20 Å2
3---2.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.95→24.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 5 298 2360
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it3.622.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.222 183 5.3 %
Rwork0.175 3257 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.222 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.175

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