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- PDB-4ddy: CTX-M-9 class A beta-lactamase complexed with compound 10 -

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Basic information

Entry
Database: PDB / ID: 4ddy
TitleCTX-M-9 class A beta-lactamase complexed with compound 10
ComponentsBeta-lactamase
KeywordsHydrolase/hydrolase inhibitor / CTX-M / molecular docking / fragment / inhibitor / Hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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-DN6 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsNichols, D.A. / Chen, Y.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Structure-Based Design of Potent and Ligand-Efficient Inhibitors of CTX-M Class A Beta-Lactamase
Authors: Nichols, D.A. / Jaishankar, P. / Larson, W. / Smith, E. / Liu, G. / Beyrouthy, R. / Bonnet, R. / Renslo, A.R. / Chen, Y.
History
DepositionJan 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details

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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)60,14517
Polymers55,9112
Non-polymers4,23415
Water9,350519
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4457
Polymers27,9551
Non-polymers1,4896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,70010
Polymers27,9551
Non-polymers2,7449
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.014, 107.105, 47.509
Angle α, β, γ (deg.)90.000, 102.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27955.463 Da / Num. of mol.: 2 / Fragment: unp 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, blaCTX-M-9b, CTX-M / Plasmid: pET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical
ChemComp-DN6 / N-[3-(1H-tetrazol-5-yl)phenyl]-3-(trifluoromethyl)benzamide


Mass: 333.268 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H10F3N5O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 38.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Potassium Phosphate, pH 8.5, vapor diffusion, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 21, 2010 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. all: 93474 / Num. obs: 92455 / % possible obs: 98.9 % / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.179 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.36-1.383.10.51742861.074192.7
1.38-1.413.40.47945371.091197.2
1.41-1.443.60.43845891.127198.3
1.44-1.473.70.41145771.177198.5
1.47-1.53.70.35146261.186198.8
1.5-1.533.70.31146171.249198.8
1.53-1.573.70.27446071.31199
1.57-1.613.80.23846221.301199.2
1.61-1.663.80.21346341.334199.3
1.66-1.713.80.19146411.388199.4
1.71-1.773.80.16246201.13199.6
1.77-1.853.80.13646501.145199.5
1.85-1.933.80.10946491.08199.7
1.93-2.033.80.08846671.158199.8
2.03-2.163.80.07646941.194199.9
2.16-2.333.80.06746681.125199.9
2.33-2.563.80.06146671.0941100
2.56-2.933.80.05546881.055199.9
2.93-3.693.80.04947151.167199.9
3.69-503.70.04647011.154198.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G35

3g35


Resolution: 1.36→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.162 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4625 5 %RANDOM
Rwork0.1708 ---
obs0.1725 92348 98.68 %-
all-93474 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 190.81 Å2 / Biso mean: 15.0039 Å2 / Biso min: 7.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å22.75 Å2
2---1.51 Å20 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 1.36→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 300 519 4707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224309
X-RAY DIFFRACTIONr_angle_refined_deg1.6562.0475884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94224.634164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98715662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.721530
X-RAY DIFFRACTIONr_chiral_restr0.1040.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213298
X-RAY DIFFRACTIONr_mcbond_it0.871.52614
X-RAY DIFFRACTIONr_mcangle_it1.33824194
X-RAY DIFFRACTIONr_scbond_it2.21231695
X-RAY DIFFRACTIONr_scangle_it3.2454.51686
X-RAY DIFFRACTIONr_rigid_bond_restr0.7424309
LS refinement shellResolution: 1.362→1.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 335 -
Rwork0.286 5983 -
all-6318 -
obs-92348 91.92 %

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