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- PDB-7u49: DFC-CTX-M-15 -

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Basic information

Entry
Database: PDB / ID: 7u49
TitleDFC-CTX-M-15
ComponentsBeta-lactamase
KeywordsSTRUCTURAL PROTEIN / antibiotics / complex / b-lactamase / DFC / CTX-M-15
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-LD0 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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)94,8336
Polymers93,5333
Non-polymers1,3013
Water2,270126
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6112
Polymers31,1781
Non-polymers4341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6112
Polymers31,1781
Non-polymers4341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6112
Polymers31,1781
Non-polymers4341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.955, 50.939, 106.597
Angle α, β, γ (deg.)90.000, 113.450, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-429-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 31177.541 Da / Num. of mol.: 3
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-LD0 / (2R,4S,5R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-oxoethyl]-5-(sulfanylmethyl)-1,3-thiazinane-4-carboxylic acid


Mass: 433.526 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H19N5O5S3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 45.96 %
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: 1.71→50 Å / Num. obs: 63310 / % possible obs: 69.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.077 / Rrim(I) all: 0.195 / Χ2: 0.676 / Net I/σ(I): 2.7 / Num. measured all: 356700
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.71-1.741.51.6622560.2861.4642.2260.3285.7
1.74-1.771.81.6114820.1711.2692.0660.43110.7
1.77-1.812.41.6658810.2881.0962.0090.39119.5
1.81-1.842.91.2511220.2580.7461.4660.39124.9
1.84-1.883.41.33814160.3440.7071.5240.41731.5
1.88-1.933.91.04117530.5970.5011.1610.42438.8
1.93-1.973.91.05221800.6090.4991.1720.4248.2
1.97-2.0340.91527220.6350.4341.0180.42859.7
2.03-2.094.10.78833000.2360.3750.8790.54973.7
2.09-2.154.40.72538280.2190.3490.8110.5284.4
2.15-2.234.90.67542230.7940.3090.7460.45792.8
2.23-2.325.60.61244800.8850.2690.670.45998.9
2.32-2.436.10.5445390.9260.2320.5890.4799.9
2.43-2.556.50.45845370.930.1930.4970.493100
2.55-2.716.60.38545230.9560.1610.4180.52100
2.71-2.9270.27945450.9770.1130.3010.55100
2.92-3.226.60.20345860.9830.0850.220.678100
3.22-3.686.70.13445960.9910.0560.1450.956100
3.68-4.646.70.09946100.9910.0410.1081.313100
4.64-506.60.07447310.9950.0320.0811.087100

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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: 1.72→48.9 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 44.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3232 1976 3.16 %
Rwork0.2584 60563 -
obs0.2604 62539 69.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.99 Å2 / Biso mean: 32.4459 Å2 / Biso min: 12.08 Å2
Refinement stepCycle: final / Resolution: 1.72→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5889 0 81 126 6096
Biso mean--52.36 33.28 -
Num. residues----786
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 (%)
1.72-1.760.751860.48912532594
1.76-1.810.4096280.416685888614
1.81-1.860.4912490.41981552160125
1.86-1.920.4245730.38782177225035
1.92-1.990.4695990.38532990308948
1.99-2.070.43831360.37424146428267
2.07-2.170.37831670.35075130529783
2.17-2.280.3611920.33855900609295
2.28-2.420.38392020.318161766378100
2.42-2.610.37272030.307162166419100
2.61-2.870.34312030.299962216424100
2.87-3.290.31642030.267862416444100
3.29-4.140.28862050.209662686473100
4.15-48.90.26342100.181764356645100

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