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- PDB-1fcn: Crystal Structure of the E. Coli AMPC Beta-Lactamase Mutant Q120L... -

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Basic information

Entry
Database: PDB / ID: 1fcn
TitleCrystal Structure of the E. Coli AMPC Beta-Lactamase Mutant Q120L/Y150E Covalently Acylated with the Substrate Beta-Lactam LORACARBEF
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / beta-lactamase beta-lactam complex / enzyme inhibitor complex
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
LORACABEF (Open form) / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsPatera, A. / Blaszczak, L.C. / Shoichet, B.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: Crystal Structures of Substrate and Inhibitor Complexes with AmpC -Lactamase: Possible Implications for Substrate-Assisted Catalysis
Authors: Patera, A. / Blaszczak, L.C. / Shoichet, B.K.
History
DepositionJul 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.6Nov 3, 2021Group: 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

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Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7814
Polymers79,0782
Non-polymers7042
Water2,270126
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8912
Polymers39,5391
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8912
Polymers39,5391
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.360, 76.264, 98.355
Angle α, β, γ (deg.)90.00, 116.00, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 39538.891 Da / Num. of mol.: 2 / Mutation: Q120L/Y150E
Source method: isolated from a genetically manipulated source
Details: INHIBITOR LORACARBEF, RESIDUE LOR, BINDS TO SER 61 BY BREAKING ITS C1-N1 LACTAM BOND
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-LOR / LORACABEF (Open form) / (3S,6R)-6-[(1S)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-3-chloro-3,4,5,6-tetrahydropyridine-2-carboxylic acid


Mass: 351.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18ClN3O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Mpotassium phosphate1reservoir
20.1 mMprotein1drop

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Data collection

DiffractionMean temperature: 129 K
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 33137 / Num. obs: 33137 / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.9
Reflection
*PLUS
% possible obs: 95 %
Reflection shell
*PLUS
% possible obs: 94.9 % / Rmerge(I) obs: 0.227

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.35→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.257 3033 10 %
Rwork0.208 --
obs-30371 95.1 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.266 Å20 Å2-6.847 Å2
2--2.677 Å20 Å2
3----1.411 Å2
Refinement stepCycle: LAST / Resolution: 2.35→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5541 0 48 126 5715
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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