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- PDB-6tzj: ADC-7 in complex with boronic acid transition state inhibitor ME_096 -

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Basic information

Entry
Database: PDB / ID: 6tzj
TitleADC-7 in complex with boronic acid transition state inhibitor ME_096
ComponentsBeta-lactamase
KeywordsHYDROLASE / inhibitor / Beta-lactamase / BATSI / ADC-7
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / Chem-PKV / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFish, E.R. / Powers, R.A. / Wallar, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI072219 United States
CitationJournal: Acs Infect Dis. / Year: 2020
Title: 1,2,3-Triazolylmethaneboronate: A Structure Activity Relationship Study of a Class of beta-Lactamase Inhibitors againstAcinetobacter baumanniiCephalosporinase.
Authors: Caselli, E. / Fini, F. / Introvigne, M.L. / Stucchi, M. / Taracila, M.A. / Fish, E.R. / Smolen, K.A. / Rather, P.N. / Powers, R.A. / Wallar, B.J. / Bonomo, R.A. / Prati, F.
History
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,02011
Polymers163,2344
Non-polymers1,7867
Water12,502694
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2743
Polymers40,8081
Non-polymers4652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1992
Polymers40,8081
Non-polymers3901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2743
Polymers40,8081
Non-polymers4652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2743
Polymers40,8081
Non-polymers4652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.477, 80.616, 105.105
Angle α, β, γ (deg.)90.000, 113.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase


Mass: 40808.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6DRA1, beta-lactamase
#2: Chemical
ChemComp-PKV / [4-[[(4-methylphenyl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]methyl-phosphonooxy-borinic acid


Mass: 390.117 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H16BN4O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ADC-7 (3mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 125707 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.049 / Rrim(I) all: 0.103 / Χ2: 1.096 / Net I/σ(I): 8.9 / Num. measured all: 532308
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.864.20.714125260.760.3920.8161.101100
1.86-1.944.20.517125030.8540.2830.591.159100
1.94-2.034.20.35125310.9220.1920.41.171100
2.03-2.134.20.244125140.9520.1340.2791.141100
2.13-2.274.20.181125330.9720.0990.2071.119100
2.27-2.444.30.142125710.9810.0770.1621.103100
2.44-2.694.30.107125200.9870.0580.1221.076100
2.69-3.084.30.099126090.9870.0530.1121.059100
3.08-3.884.30.077126240.9920.0410.0871.033100
3.88-504.20.056127760.9950.0310.0641.00399.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0T

4u0t


Resolution: 1.8→44.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.453 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 6333 5 %RANDOM
Rwork0.1937 ---
obs0.1959 119353 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: 100.01 Å2 / Biso mean: 34.905 Å2 / Biso min: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å21.25 Å2
2---2.42 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.8→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10979 0 100 713 11792
Biso mean--58.29 39.7 -
Num. residues----1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01211383
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.65815528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78151425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51924.851505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.854151798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6091523
X-RAY DIFFRACTIONr_chiral_restr0.1050.21505
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028664
LS refinement shellResolution: 1.8→1.845 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.314 438 -
Rwork0.27 8631 -
obs--97.04 %

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