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- PDB-3g30: CTX-M-9 class A beta-lactamase complexed with compound 3 (G30) -

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Basic information

Entry
Database: PDB / ID: 3g30
TitleCTX-M-9 class A beta-lactamase complexed with compound 3 (G30)
ComponentsBeta-lactamase CTX-M-9a
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CTX-M / beta-lactamase / molecular docking / fragment / inhibitor / Antibiotic resistance / Hydrolase / Plasmid / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-G30 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, Y. / Shoichet, B.K.
CitationJournal: Nat.Chem.Biol. / Year: 2009
Title: Molecular docking and ligand specificity in fragment-based inhibitor discovery
Authors: Chen, Y. / Shoichet, B.K.
History
DepositionFeb 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
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 CTX-M-9a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6964
Polymers27,9721
Non-polymers7243
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.803, 41.803, 230.542
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactamase CTX-M-9a / Beta-lactamase / CTX-M-9 beta-lactamase / Betalactamase CTX-M-9


Mass: 27972.494 Da / Num. of mol.: 1 / Fragment: sequence database residues 29-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-9, blaCTX-M-9a, CTX-M / Plasmid: PET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical ChemComp-G30 / (1S,2R)-2-[(2,5-difluorophenyl)carbamoyl]cyclopropanecarboxylic acid


Mass: 241.191 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H9F2NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Jul 28, 2008 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 22863 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Χ2: 1.039
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.865.90.79221671.01798.5
1.86-1.947.40.66122271.04899.6
1.94-2.037.70.44322271.04399.8
2.03-2.137.70.32222581.01999.8
2.13-2.277.70.23522530.98899.8
2.27-2.447.70.17822690.987100
2.44-2.697.70.12622721.015100
2.69-3.087.60.09423051.053100
3.08-3.887.50.06223461.08499.9
3.88-506.90.03125391.13499.6

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Processing

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

1ylj


Resolution: 1.8→38.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.811 / SU B: 3.438 / SU ML: 0.107 / SU R Cruickshank DPI: 0.158 / SU Rfree: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1135 5 %RANDOM
Rwork0.208 ---
obs0.21 22803 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.11 Å2 / Biso mean: 25.36 Å2 / Biso min: 7.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.48 Å20 Å2
2--0.97 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 51 157 2205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222088
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9962857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44824.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16415344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.031517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021594
X-RAY DIFFRACTIONr_nbd_refined0.2080.21024
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.214
X-RAY DIFFRACTIONr_mcbond_it1.0911.51370
X-RAY DIFFRACTIONr_mcangle_it1.62422134
X-RAY DIFFRACTIONr_scbond_it2.4073825
X-RAY DIFFRACTIONr_scangle_it3.6214.5706
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 68 -
Rwork0.294 1515 -
all-1583 -
obs--97.3 %

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