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- PDB-7u57: apo-CTX-M-15 -

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Basic information

Entry
Database: PDB / ID: 7u57
Titleapo-CTX-M-15
ComponentsBeta-lactamase
KeywordsSTRUCTURAL PROTEIN / antibiotics / apo / b-lactamase / CTX-M-15
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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
DepositionMar 1, 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 1.2Mar 19, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details
Item: _pdbx_database_related.content_type / _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)93,8546
Polymers93,5663
Non-polymers2883
Water3,513195
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2852
Polymers31,1891
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2852
Polymers31,1891
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2852
Polymers31,1891
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.079, 51.033, 106.863
Angle α, β, γ (deg.)90.000, 112.590, 90.000
Int Tables number5
Space group name H-MC121

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.05 Å3/Da / Density % sol: 59.73 %
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: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→51.71 Å / Num. obs: 74931 / % possible obs: 75 % / Redundancy: 1.2 % / Biso Wilson estimate: 35.37 Å2 / CC1/2: 0.935 / Χ2: 20.394 / Net I/σ(I): 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2% possible allRmerge(I) obsRpim(I) allΧ2
1.73-1.76110.935
1.76-1.7990.935
1.79-1.8380.935
1.83-1.86120.935
1.95-2130.93530
2-2.05130.93530
2.05-2.11110.935
2.11-2.1810.935
2.26-2.35120.935
2.35-2.45120.935
2.45-2.58130.93530
2.58-2.75130.935
2.75-2.96150.935
2.96-3.26130.935
3.26-3.73110.935
3.73-4.691.4140.9350.980.95316.612
4.69-91.2710.3131.22621.744

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBT

4hbt


Resolution: 2.37→51.71 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3268 1271 3.65 %
Rwork0.2221 33509 -
obs0.226 34780 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.87 Å2 / Biso mean: 46.5251 Å2 / Biso min: 15.51 Å2
Refinement stepCycle: final / Resolution: 2.37→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 15 195 6144
Biso mean--60.43 42.15 -
Num. residues----792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.37-2.460.33881380.25983606374497
2.46-2.580.33281390.28413658379799
2.58-2.710.45491400.300137263866100
2.71-2.880.39461410.272237103851100
2.88-3.110.35711420.25237223864100
3.11-3.420.32011410.250437643905100
3.42-3.910.3861410.21223685382699
3.91-4.930.28051410.17173752389399
4.93-51.710.24331480.17938864034100

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