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

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Basic information

Entry
Database: PDB / ID: 3grj
TitleAmpC beta-lactamase in complex with Fragment-based Inhibitor
ComponentsBeta-lactamase
KeywordsHydrolase/Hydrolase Inhibitor / Antibiotic resistance / Hydrolase / 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
2-phenyl-1H-imidazole-4-carboxylic acid / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 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 25, 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 1.3Sep 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)80,86317
Polymers79,1762
Non-polymers1,68715
Water4,414245
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3557
Polymers39,5881
Non-polymers7676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,50810
Polymers39,5881
Non-polymers9209
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.508, 76.811, 98.005
Angle α, β, γ (deg.)90.000, 116.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 260 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-G14 / 2-phenyl-1H-imidazole-4-carboxylic acid


Mass: 188.183 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H8N2O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 400 mM KPi at pH 8.5 with 25% PEG 3350, at 294K, VAPOR DIFFUSION, HANGING DROP

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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: Jun 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 30971 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.133 / Χ2: 3.488
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.493.10.52430021.90296.8
2.49-2.593.40.49430591.88599.4
2.59-2.73.60.44830971.89399.9
2.7-2.853.70.35930962.163100
2.85-3.023.70.28730802.908100
3.02-3.263.70.21231063.598100
3.26-3.583.70.15331144.403100
3.58-4.13.60.11230964.7999.9
4.1-5.173.60.08231364.5199.8
5.17-503.70.08631856.14499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.27 Å
Translation2.5 Å45.27 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KE4

1ke4


Resolution: 2.49→45.27 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 11.017 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.005 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1368 5 %RANDOM
Rwork0.193 ---
obs0.196 27340 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.5 Å2 / Biso mean: 41.99 Å2 / Biso min: 26.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.39 Å2
2---0.08 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.49→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5771 0 84 273 6128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226069
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9618325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.235774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48224.636261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68415970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7221527
X-RAY DIFFRACTIONr_chiral_restr0.1860.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024687
X-RAY DIFFRACTIONr_nbd_refined0.2260.23021
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24111
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2333
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.211
X-RAY DIFFRACTIONr_mcbond_it0.7691.53762
X-RAY DIFFRACTIONr_mcangle_it1.02125966
X-RAY DIFFRACTIONr_scbond_it1.7332732
X-RAY DIFFRACTIONr_scangle_it2.3644.52329
LS refinement shellResolution: 2.49→2.552 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 95 -
Rwork0.253 1747 -
all-1842 -
obs--89.94 %

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