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- PDB-6tzi: ADC-7 in complex with boronic acid transition state inhibitor PFC_001 -

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Basic information

Entry
Database: PDB / ID: 6tzi
TitleADC-7 in complex with boronic acid transition state inhibitor PFC_001
ComponentsBeta-lactamase
KeywordsHYDROLASE / inhibitor / Beta-lactamase / BATSI / ADC-7
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
Chem-P1K / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.744 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 30, 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)164,7628
Polymers163,2344
Non-polymers1,5284
Water15,691871
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1912
Polymers40,8081
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1912
Polymers40,8081
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1912
Polymers40,8081
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1912
Polymers40,8081
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.928, 81.103, 105.938
Angle α, β, γ (deg.)90.000, 113.060, 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-P1K / phosphonooxy-[[4-[[2,2,2-tris(fluoranyl)ethylsulfonylamino]methyl]-1,2,3-triazol-1-yl]methyl]borinic acid


Mass: 382.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11BF3N4O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
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-D / Wavelength: 1.07809 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07809 Å / Relative weight: 1
ReflectionResolution: 1.744→81.95 Å / Num. obs: 116473 / % possible obs: 96 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.053 / Rrim(I) all: 0.098 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.935-1.9413.60.55234469660.7920.3430.652298.9
8.978-81.823.40.046364010760.9960.0290.05519.898.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0X

4u0x


Resolution: 1.744→81.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.223 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.17
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 5806 5 %RANDOM
Rwork0.216 ---
obs0.2188 110727 82.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.8 Å2 / Biso mean: 40.112 Å2 / Biso min: 18.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.02 Å2
2---0.16 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.744→81.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11061 0 115 895 12071
Biso mean--55.48 43.83 -
Num. residues----1423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211449
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.6615613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5835.0181421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4825.049513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.188151861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7051522
X-RAY DIFFRACTIONr_chiral_restr0.1130.21508
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028723
LS refinement shellResolution: 1.744→1.789 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 102 -
Rwork0.297 1828 -
all-1930 -
obs--18.64 %

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