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- PDB-3g34: CTX-M-9 class A beta-lactamase complexed with compound 11 (1CE) -

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Basic information

Entry
Database: PDB / ID: 3g34
TitleCTX-M-9 class A beta-lactamase complexed with compound 11 (1CE)
ComponentsBeta-lactamase CTX-M-9a
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CTX-M / beta-lactamase / molecular docking / fragment / inhibitor / Antibiotic resistance / 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-1CE / PHOSPHATE ION / 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 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
B: Beta-lactamase CTX-M-9a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,52311
Polymers55,9452
Non-polymers1,5789
Water11,746652
1
A: Beta-lactamase CTX-M-9a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4344
Polymers27,9721
Non-polymers4613
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)29,0897
Polymers27,9721
Non-polymers1,1166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.141, 106.886, 47.445
Angle α, β, γ (deg.)90.000, 101.630, 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: 27972.494 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-1CE / 3-(1H-tetrazol-5-ylmethyl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one


Mass: 288.328 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H12N6OS
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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 Å3/Da / Density % sol: 38.62 %
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: Jun 21, 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: 106102 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.056 / Χ2: 1.044
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.31-1.363.60.274105911.04699.9
1.36-1.413.80.228105861.003100
1.41-1.483.80.179105561.008100
1.48-1.553.90.144106310.998100
1.55-1.653.90.111105671.017100
1.65-1.783.90.09106021.063100
1.78-1.963.90.074106261.005100
1.96-2.243.80.062106021.091100
2.24-2.823.80.054106531.071100
2.82-5040.036106881.1399.6

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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: 1.31→29.22 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.908 / SU B: 1.392 / SU ML: 0.028 / SU R Cruickshank DPI: 0.06 / SU Rfree: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 5305 5 %RANDOM
Rwork0.155 ---
obs0.156 106059 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.84 Å2 / Biso mean: 13.089 Å2 / Biso min: 4.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.49 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.31→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 0 102 652 4805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224244
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9955818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7895572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55324.545176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50715706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6191534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023234
X-RAY DIFFRACTIONr_nbd_refined0.1880.22237
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23005
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.090.2521
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.279
X-RAY DIFFRACTIONr_mcbond_it0.6361.52743
X-RAY DIFFRACTIONr_mcangle_it1.01524344
X-RAY DIFFRACTIONr_scbond_it1.47131752
X-RAY DIFFRACTIONr_scangle_it2.1314.51451
X-RAY DIFFRACTIONr_rigid_bond_restr0.8634495
X-RAY DIFFRACTIONr_sphericity_free2.3333652
X-RAY DIFFRACTIONr_sphericity_bonded1.76234153
LS refinement shellResolution: 1.31→1.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 352 -
Rwork0.204 7227 -
all-7579 -
obs--96.71 %

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