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- PDB-4len: CTX-M-9 in complex with the broad spectrum inhibitor 3-(2- carbox... -

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Basic information

Entry
Database: PDB / ID: 4len
TitleCTX-M-9 in complex with the broad spectrum inhibitor 3-(2- carboxyvinyl)benzo(b)thiophene-2-boronic acid
ComponentsBeta-lactamase
Keywordshydrolase/hydrolase inhibitor / Binding Sites / structure base drug design / Drug Discovery / Molecular / Enzyme Inhibitors / beta lactamases / boronic acids / broad spectrum / bacterial resistance / double perturbation cycle analysis / thermodynamics / structure activity relationship / 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-2GK / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTondi, D.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Targeting Class A and C Serine beta-Lactamases with a Broad-Spectrum Boronic Acid Derivative.
Authors: Tondi, D. / Venturelli, A. / Bonnet, R. / Pozzi, C. / Shoichet, B.K. / Costi, M.P.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Oct 19, 2016Group: Structure summary
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 20, 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)56,4414
Polymers55,9452
Non-polymers4962
Water13,944774
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2212
Polymers27,9721
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2212
Polymers27,9721
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.116, 106.595, 47.680
Angle α, β, γ (deg.)90.00, 102.03, 90.00
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: 27972.494 Da / Num. of mol.: 2 / Fragment: CTX-M9 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Gene: blaCTX-M-9, blaCTX-M-9a, blaCTX-M-9a blaCTX-M-9 blaCTX-M-9b, blaCTX-M-9b
Plasmid: pET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical ChemComp-2GK / (2E)-3-[2-(dihydroxyboranyl)-1-benzothiophen-3-yl]prop-2-enoic acid


Mass: 248.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9BO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE STARTING MATERIAL USED FOR CHEMICAL REACTION CORRESPONDS TO THE COMPUND: 3-[2-(4,4,5,5- ...THE STARTING MATERIAL USED FOR CHEMICAL REACTION CORRESPONDS TO THE COMPUND: 3-[2-(4,4,5,5-TETRAMETHYL-[1,3,2]DIOXABOROLAN-2-YL)-BENZO[B]THIOPHEN-3-YL]-ACRYLIC ACID. SEE ALSO LINK RECORDS.

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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: 38.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 1.4 M potassium phosphate buffer using microseeding techniques, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 8.8

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 1, 2004 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.35→20 Å / Num. all: 82707 / Num. obs: 82595 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YM1

1ym1


Resolution: 1.5→19.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.114 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18174 3455 5 %RANDOM
Rwork0.15935 ---
obs0.16048 65055 97.48 %-
all-82707 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.214 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 34 774 4715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9775589
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08524.578166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68615683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0061531
X-RAY DIFFRACTIONr_chiral_restr0.0850.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213089
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4140.7692133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7531.1482665
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4480.8581964
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 223 -
Rwork0.18 4329 -
obs--88.22 %

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