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

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3gsg
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-GF1 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)80,90917
Polymers79,1762
Non-polymers1,73415
Water11,746652
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5999
Polymers39,5881
Non-polymers1,0118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3118
Polymers39,5881
Non-polymers7237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.594, 75.930, 97.659
Angle α, β, γ (deg.)90.000, 116.370, 90.000
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


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GF1 / (2S)-2-[(3aR,4R,7S,7aS)-1,3-dioxooctahydro-2H-4,7-methanoisoindol-2-yl]propanoic acid


Mass: 237.252 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H15NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 298 K / pH: 8.7
Details: 1.7M potassium phosphate, pH 8.7, 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
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→45.3 Å / Num. obs: 52364 / % possible obs: 99.7 %
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.6 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.26 Å
Translation2.5 Å45.26 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KE4

1ke4


Resolution: 2.1→45.27 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 0 / SU B: 5.515 / SU ML: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.244 2263 5 %
Rwork0.191 --
obs0.194 45418 99.9 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 25.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.05 Å2
2--0.04 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5792 0 104 652 6548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.968240
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95424.778270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53815956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7151528
X-RAY DIFFRACTIONr_chiral_restr0.2910.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024644
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.23126
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24120
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2566
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6061.53739
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79425900
X-RAY DIFFRACTIONr_scbond_it1.18732716
X-RAY DIFFRACTIONr_scangle_it1.6444.52336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å
RfactorNum. reflection% reflection
Rfree0.26 156 -
Rwork0.23 3173 -
obs--100 %

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