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- PDB-3g2y: CTX-M-9 class A beta-lactamase complexed with compound 1 (GF4) -

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Basic information

Entry
Database: PDB / ID: 3g2y
TitleCTX-M-9 class A beta-lactamase complexed with compound 1 (GF4)
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-GF4 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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 2.0Dec 25, 2019Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Polymer sequence
Category: atom_site / entity_poly ...atom_site / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _atom_site.occupancy / _entity_poly.pdbx_seq_one_letter_code_can ..._atom_site.occupancy / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase CTX-M-9a
B: Beta-lactamase CTX-M-9a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3775
Polymers55,9112
Non-polymers4673
Water11,043613
1
A: Beta-lactamase CTX-M-9a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1502
Polymers27,9551
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase CTX-M-9a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2283
Polymers27,9551
Non-polymers2722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.154, 106.877, 47.703
Angle α, β, γ (deg.)90.000, 101.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27955.463 Da / Num. of mol.: 2 / 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-GF4 / 4-ethyl-5-methyl-2-(1H-tetrazol-5-yl)-1,2-dihydro-3H-pyrazol-3-one


Mass: 194.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N6O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.94 %
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: Apr 11, 2008 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.31→50 Å / Num. obs: 96638 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.056 / Χ2: 1.025
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.31-1.361.70.244101971.07696.7
1.36-1.411.70.198101781.06496.9
1.41-1.481.80.156101460.99996.7
1.48-1.551.80.128101301.02696.1
1.55-1.651.80.101100090.98295.2
1.65-1.781.80.08399331.0194.4
1.78-1.961.80.06897981.06592.7
1.96-2.241.80.05394440.98389.7
2.24-2.821.80.04691230.96886.1
2.82-5020.04376801.08472.1

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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: 1.31→23.19 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.183 / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.898 / SU B: 1.629 / SU ML: 0.032 / SU R Cruickshank DPI: 0.068 / SU Rfree: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4828 5 %RANDOM
Rwork0.161 ---
obs0.162 96597 91.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.74 Å2 / Biso mean: 13.034 Å2 / Biso min: 2.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.42 Å2
2---0.21 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.31→23.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 32 613 4712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224181
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9775720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7445569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50524.171175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72415710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1061537
X-RAY DIFFRACTIONr_chiral_restr0.0750.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023191
X-RAY DIFFRACTIONr_nbd_refined0.1890.22103
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2476
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.264
X-RAY DIFFRACTIONr_mcbond_it0.6581.52755
X-RAY DIFFRACTIONr_mcangle_it1.04324345
X-RAY DIFFRACTIONr_scbond_it1.52731575
X-RAY DIFFRACTIONr_scangle_it2.2484.51356
X-RAY DIFFRACTIONr_rigid_bond_restr0.79434330
X-RAY DIFFRACTIONr_sphericity_free2.5183613
X-RAY DIFFRACTIONr_sphericity_bonded1.67434097
LS refinement shellResolution: 1.31→1.345 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 376 -
Rwork0.219 6878 -
all-7254 -
obs--93.52 %

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