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- PDB-1fsy: AMPC BETA-LACTAMASE FROM E. COLI COMPLEXED WITH INHIBITOR CLOXACI... -

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Basic information

Entry
Database: PDB / ID: 1fsy
TitleAMPC BETA-LACTAMASE FROM E. COLI COMPLEXED WITH INHIBITOR CLOXACILLINBORONIC ACID
ComponentsCEPHALOSPORINASE
KeywordsHYDROLASE / cephalosporinase / beta-lactamase / serine hydrolase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-105 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsCaselli, E. / Powers, R.A. / Blasczcak, L.C. / Wu, C.Y. / Prati, F. / Shoichet, B.K.
CitationJournal: Chem.Biol. / Year: 2001
Title: Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases.
Authors: Caselli, E. / Powers, R.A. / Blasczcak, L.C. / Wu, C.Y. / Prati, F. / Shoichet, B.K.
History
DepositionSep 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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: CEPHALOSPORINASE
B: CEPHALOSPORINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7465
Polymers79,0622
Non-polymers6843
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-21 kcal/mol
Surface area27840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.360, 77.570, 97.460
Angle α, β, γ (deg.)90.00, 116.18, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein CEPHALOSPORINASE / E.C.3.5.2.6 / BETA-LACTAMASE


Mass: 39530.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SER 64 BINDS TO BORON OF LIGAND 105 IN BOTH CHAINS / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-105 / N-[5-METHYL-3-O-TOLYL-ISOXAZOLE-4-CARBOXYLIC ACID AMIDE] BORONIC ACID / CLOXACILLIN DERIVATIVE


Mass: 294.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12BClN2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate, 95 uM AmpC, 586 uM cloxacillinboronic acid, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Mpotassium phosphate1reservoir
20.095 mMprotein1drop
32 %DMSO1drop
41.7 Mpotassium phosphate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: May 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 79142 / Num. obs: 79142 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 25.06 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.9
Reflection shellResolution: 1.75→1.79 Å / Rmerge(I) obs: 0.139 / Num. unique all: 5036 / % possible all: 94.6
Reflection
*PLUS
Num. measured all: 287631
Reflection shell
*PLUS
% possible obs: 94.6 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 7740 10 %random
Rwork0.196 ---
all-77033 --
obs-77033 96.6 %-
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5592 0 45 499 6136
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.78
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_improper_angle_d1.1
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
LS refinement shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.79 Å

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