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- PDB-9c83: X-ray crystal structure of AmpC beta-lactamase with inhibitor -

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Basic information

Entry
Database: PDB / ID: 9c83
TitleX-ray crystal structure of AmpC beta-lactamase with inhibitor
ComponentsAmpC Beta-lactamase
KeywordsHYDROLASE / inhibitor
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/transpeptidase-like
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLiu, F. / Shoichet, B.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Improved correlations with score, hit-rate, and affinity as docking library and testing scale increase
Authors: Liu, F. / Shoichet, B.K. / Bassim, V.
History
DepositionJun 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,9324
Polymers83,1872
Non-polymers7462
Water00
1
A: AmpC Beta-lactamase
hetero molecules


  • defined by author
  • 42 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)41,9662
Polymers41,5931
Non-polymers3731
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AmpC Beta-lactamase
hetero molecules


  • defined by author
  • 42 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)41,9662
Polymers41,5931
Non-polymers3731
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.774, 77.030, 100.079
Angle α, β, γ (deg.)90.000, 115.470, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein AmpC Beta-lactamase / Cephalosporinase / CSase


Mass: 41593.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampC, ampA, b4150, JW4111 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-A1AUZ / N-[(3M)-3-(5-chloro-1,2,3-thiadiazol-4-yl)phenyl]-5-methyl-3-oxo-2,3-dihydro-1,2-oxazole-4-sulfonamide


Mass: 372.807 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9ClN4O4S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2M KPI; pH 8.56

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 21, 2023
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.9→58.87 Å / Num. obs: 35902 / % possible obs: 98.62 % / Redundancy: 1.977 % / Biso Wilson estimate: 30.38 Å2 / CC1/2: 0.837 / CC star: 0.955 / Rmerge(I) obs: 0.1716 / Net I/σ(I): 2.88
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.1993 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 1644 / CC1/2: 0.828 / CC star: 0.952 / % possible all: 89.15

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→58.87 Å / SU ML: 0.5793 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.2359
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3773 1817 10.01 %
Rwork0.3075 16339 -
obs0.3145 18156 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.54 Å2
Refinement stepCycle: LAST / Resolution: 2.9→58.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 46 0 5531
Refine LS restraintsType: f_bond_d / Dev ideal: 0.0112 / Number: 5693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.39391200.33441075X-RAY DIFFRACTION85.36
2.98-3.070.36081410.29091266X-RAY DIFFRACTION99.93

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