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- PDB-9c8j: X-ray crystal structure of AmpC beta-lactamase with inhibitor -

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Basic information

Entry
Database: PDB / ID: 9c8j
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: 1.55 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.
History
DepositionJun 12, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,9204
Polymers83,1872
Non-polymers7342
Water10,953608
1
A: AmpC Beta-lactamase
hetero molecules


  • defined by author
  • 42 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)41,9602
Polymers41,5931
Non-polymers3671
Water181
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)41,9602
Polymers41,5931
Non-polymers3671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.230, 76.900, 97.690
Angle α, β, γ (deg.)90.000, 116.540, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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-A1AU5 / N-(1-acetyl-2,3-dihydro-1H-indol-4-yl)-3-chloro-2-hydroxybenzene-1-sulfonamide


Mass: 366.819 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C16H15ClN2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.5 %
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: 1.55→58.45 Å / Num. obs: 112725 / % possible obs: 99.31 % / Redundancy: 1.99 % / Biso Wilson estimate: 23.36 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02917 / Net I/σ(I): 14.17
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.8336 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 10870 / CC1/2: 0.439 / CC star: 0.781 / % possible all: 95.75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→58.45 Å / SU ML: 0.2061 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9486
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 1715 1.52 %
Rwork0.1846 110961 -
obs0.185 112676 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.32 Å2
Refinement stepCycle: LAST / Resolution: 1.55→58.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5598 0 48 608 6254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00935941
X-RAY DIFFRACTIONf_angle_d1.08028144
X-RAY DIFFRACTIONf_chiral_restr0.0805870
X-RAY DIFFRACTIONf_plane_restr0.0081057
X-RAY DIFFRACTIONf_dihedral_angle_d17.04662156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.39691370.35748851X-RAY DIFFRACTION95.15
1.6-1.650.36631420.34089178X-RAY DIFFRACTION99.37
1.65-1.710.31921430.31399262X-RAY DIFFRACTION99.7
1.71-1.770.28981430.25949252X-RAY DIFFRACTION99.71
1.77-1.860.26811430.2259280X-RAY DIFFRACTION99.86
1.86-1.950.25071440.20519243X-RAY DIFFRACTION99.85
1.95-2.080.21111430.20019295X-RAY DIFFRACTION99.81
2.08-2.240.21521430.17829254X-RAY DIFFRACTION99.77
2.24-2.460.2151430.18629300X-RAY DIFFRACTION99.86
2.46-2.820.20771450.19099331X-RAY DIFFRACTION99.89
2.82-3.550.20541430.179299X-RAY DIFFRACTION99.56
3.55-58.450.17721460.14499416X-RAY DIFFRACTION99.29

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