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- PDB-1kvl: X-ray Crystal Structure of AmpC S64G Mutant beta-Lactamase in Com... -

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Basic information

Entry
Database: PDB / ID: 1kvl
TitleX-ray Crystal Structure of AmpC S64G Mutant beta-Lactamase in Complex with Substrate and Product Forms of Cephalothin
ComponentsBeta-lactamase
KeywordsHYDROLASE / amide hydrolase / beta-lactamase / cephalothin / substrate-enzyme complex / product-enzyme complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
CEPHALOTHIN / Chem-KCP / PHOSPHATE ION / Chem-THN / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsBeadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K.
CitationJournal: Structure / Year: 2002
Title: Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase.
Authors: Beadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K.
History
DepositionJan 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)80,4137
Polymers79,1162
Non-polymers1,2975
Water8,791488
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5015
Polymers39,5581
Non-polymers9434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9122
Polymers39,5581
Non-polymers3541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.619, 77.153, 98.066
Angle α, β, γ (deg.)90.00, 115.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39557.895 Da / Num. of mol.: 2 / Mutation: S64G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase

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Non-polymers , 5 types, 493 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-KCP / 2-[CARBOXY-(2-THIOPHEN-2-YL-ACETYLAMINO)-METHYL]-5-METHYL-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / HYDROLYZED CEPHALOTHIN


Mass: 356.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O5S2
#4: Chemical ChemComp-CLS / CEPHALOTHIN / 3-ACETOXYMETHYL-8-OXO-7-(2-THIOPHEN-2-YL-ACETYLAMINO)-5-THIA-1-AZA-BICYCLO[4.2.0]OCT-2-ENE-2-CARBOXYLIC ACID


Mass: 396.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N2O6S2 / Comment: antibiotic*YM
#5: Chemical ChemComp-THN / 2-[CARBOXY-(2-THIOPHEN-2-YL-ACETYLAMINO)-METHYL]-5-METHYLENE-5,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / HYDROLYZED CEPHALOTHIN


Mass: 354.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O5S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate; the crystal was then soaked in saturated cephalothin in crystallizing buffer for 3 hours, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
Conc.: 1.7 M / Common name: potassium phosphate / Details: pH8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→20 Å / Num. obs: 108082 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 28.2
Reflection shellResolution: 1.53→1.57 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.14 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 385475
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C3B

1c3b


Resolution: 1.53→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.22 2220 Random
Rwork0.195 --
all-108082 -
obs-89700 -
Solvent computationksol: 0.383662 e/Å3
Displacement parametersBiso mean: 54.1656 Å2
Baniso -1Baniso -2Baniso -3
1--3.573 Å20 Å2-4.646 Å2
2--2.884 Å20 Å2
3---0.689 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5553 0 105 488 6146
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_mcbond_it1.2631.5
X-RAY DIFFRACTIONc_scbond_it2.1022
X-RAY DIFFRACTIONc_mcangle_it1.8352
X-RAY DIFFRACTIONc_scangle_it3.0822.5
LS refinement shellResolution: 1.53→1.58 Å
RfactorNum. reflection
Rfree0.223 184
Rwork0.213 -
obs-6960
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cephalothin.paramcephalothin.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 2.5 % / Rfactor obs: 0.195 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
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
Lowest resolution: 1.57 Å

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