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- PDB-7u48: Clavulanic acid-CTX-M-15 -

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Basic information

Entry
Database: PDB / ID: 7u48
TitleClavulanic acid-CTX-M-15
ComponentsBeta-lactamase
KeywordsSTRUCTURAL PROTEIN / Inhibitor / complex / bacterial resistance / B-lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane
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
Chem-LBX / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsAhmadvand, P. / Kang, C.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1804699 United States
CitationJournal: Int J Mol Sci / Year: 2022
Title: Characterization of Interactions between CTX-M-15 and Clavulanic Acid, Desfuroylceftiofur, Ceftiofur, Ampicillin, and Nitrocefin.
Authors: Ahmadvand, P. / Avillan, J.J. / Lewis, J.A. / Call, D.R. / Kang, C.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,73812
Polymers93,5663
Non-polymers1,1729
Water6,756375
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6705
Polymers31,1891
Non-polymers4814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4863
Polymers31,1891
Non-polymers2972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5824
Polymers31,1891
Non-polymers3933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.692, 50.976, 106.699
Angle α, β, γ (deg.)90.000, 113.230, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-522-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 31188.607 Da / Num. of mol.: 3 / Mutation: A25P, Q26L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaCTX-M-15 / Production host: Escherichia coli (E. coli) / References: UniProt: C7S9T0, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LBX / (E)-5-hydroxy-3-oxo-N-(3-oxopropylidene)-L-norvaline


Mass: 201.177 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 300 mM Ammonium sulfate, 30% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 83707 / % possible obs: 84.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.101 / Rrim(I) all: 0.185 / Χ2: 1.698 / Net I/σ(I): 4.1 / Num. measured all: 252076
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.67-1.71.71.2248290.2531.0021.590.42916.9
1.7-1.731.81.27312520.3350.9841.6180.41925.7
1.73-1.761.91.31820410.2511.0341.6850.44341.3
1.76-1.821.27528140.3140.9921.6240.41357.9
1.8-1.842.21.16136410.3520.8491.4460.42773.7
1.84-1.882.51.14843030.3590.7951.4030.52787.9
1.88-1.932.70.92246640.5470.6381.1270.45995.2
1.93-1.982.90.79748750.6140.5430.9680.47498.2
1.98-2.043.10.65548330.7070.4340.7890.49999.1
2.04-2.13.20.5148830.8150.3320.610.54399.4
2.1-2.183.20.41348970.8490.270.4950.61199.4
2.18-2.273.30.34848920.8780.2230.4140.69199.6
2.27-2.373.20.29549400.9010.1920.3530.78699.8
2.37-2.493.20.23149150.9340.1510.2771.04599.6
2.49-2.653.30.20749050.9320.1360.2491.30199.3
2.65-2.863.40.18249540.9480.1150.2161.69799.8
2.86-3.143.30.15649550.9560.1030.1882.44999.9
3.14-3.63.30.13549760.9570.0880.1623.84799.9
3.6-4.533.30.12649930.9590.0810.155.57100
4.53-503.30.10451450.9690.0690.1254.46199.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBT

4hbt


Resolution: 1.67→49.02 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 1946 2.39 %
Rwork0.2502 79458 -
obs0.2511 81404 82.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 263.82 Å2 / Biso mean: 43.1163 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 1.67→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 74 375 6383
Biso mean--82 45.21 -
Num. residues----792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.67-1.710.4555270.44593796414
1.71-1.760.4235430.41311708175125
1.76-1.810.4082790.39423367344649
1.81-1.870.39381250.38375164528976
1.87-1.930.381590.36396485664494
1.93-2.010.35321660.34276722688899
2.01-2.10.34311650.31646775694099
2.1-2.210.33981680.2946839700799
2.21-2.350.32831670.291468347001100
2.35-2.530.33441670.2796829699699
2.53-2.790.30011690.28556874704399
2.79-3.190.31361690.264169097078100
3.19-4.020.27661690.221169037072100
4.02-49.020.20281730.183271127285100

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