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- PDB-3gtc: AmpC beta-lactamase in complex with Fragment-based Inhibitor -

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Basic information

Entry
Database: PDB / ID: 3gtc
TitleAmpC beta-lactamase in complex with Fragment-based Inhibitor
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / Antibiotic resistance / Periplasm / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GTC / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsTeotico, D.T. / Shoichet, B.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Docking for fragment inhibitors of AmpC beta-lactamase
Authors: Teotico, D.G. / Babaoglu, K. / Rocklin, G.J. / Ferreira, R.S. / Giannetti, A.M. / Shoichet, B.K.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5029
Polymers79,1762
Non-polymers1,3267
Water12,520695
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2325
Polymers39,5881
Non-polymers6454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2704
Polymers39,5881
Non-polymers6823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.447, 77.951, 97.881
Angle α, β, γ (deg.)90.00, 115.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GTC / (1R,2S)-2-(5-thioxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)cyclohexanecarboxylic acid


Mass: 227.283 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H13N3O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 62779 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Χ2: 1.325
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.973.70.37461851.41897.8
1.97-2.053.80.28761960.83398.1
2.05-2.143.80.19162010.85198.3
2.14-2.253.80.20762031.67498.5
2.25-2.393.80.17162701.66898.8
2.39-2.583.80.09362651.10399
2.58-2.843.80.07263241.18499.3
2.84-3.253.80.04963261.399.4
3.25-4.093.70.03963501.70799.7
4.09-503.70.03264591.54299.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.847 / SU B: 4.176 / SU ML: 0.121 / SU R Cruickshank DPI: 0.432 / SU Rfree: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3184 5.1 %RANDOM
Rwork0.205 ---
obs0.207 62685 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.08 Å2 / Biso mean: 25.94 Å2 / Biso min: 10.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.37 Å2
2--0.21 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5615 0 85 695 6395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225865
X-RAY DIFFRACTIONr_bond_other_d0.0010.023908
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9638018
X-RAY DIFFRACTIONr_angle_other_deg0.92839581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8995718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73324.818247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64415915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9791522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021114
X-RAY DIFFRACTIONr_nbd_refined0.1960.21197
X-RAY DIFFRACTIONr_nbd_other0.1790.23992
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22853
X-RAY DIFFRACTIONr_nbtor_other0.0820.22862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2548
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.220
X-RAY DIFFRACTIONr_mcbond_it0.7071.54603
X-RAY DIFFRACTIONr_mcbond_other0.0891.51440
X-RAY DIFFRACTIONr_mcangle_it0.80325790
X-RAY DIFFRACTIONr_scbond_it1.15732788
X-RAY DIFFRACTIONr_scangle_it1.6734.52228
LS refinement shellResolution: 1.9→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 208 -
Rwork0.307 4267 -
all-4475 -
obs--96.74 %

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