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- PDB-6tzf: ADC-7 in complex with boronic acid transition state inhibitor S17079 -

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Basic information

Entry
Database: PDB / ID: 6tzf
TitleADC-7 in complex with boronic acid transition state inhibitor S17079
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
Chem-KAS / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,5428
Polymers163,2344
Non-polymers1,3084
Water5,945330
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1352
Polymers40,8081
Non-polymers3271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1352
Polymers40,8081
Non-polymers3271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1352
Polymers40,8081
Non-polymers3271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1352
Polymers40,8081
Non-polymers3271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.624, 80.785, 107.003
Angle α, β, γ (deg.)90.000, 112.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROILEILEAA3 - 3575 - 359
21PROPROILEILEBB3 - 3575 - 359
12LYSLYSALAALAAA4 - 3566 - 358
22LYSLYSALAALACC4 - 3566 - 358
13PROPROILEILEAA3 - 3575 - 359
23PROPROILEILEDD3 - 3575 - 359
14LYSLYSALAALABB4 - 3566 - 358
24LYSLYSALAALACC4 - 3566 - 358
15PROPROLYSLYSBB3 - 3585 - 360
25PROPROLYSLYSDD3 - 3585 - 360
16LYSLYSALAALACC4 - 3566 - 358
26LYSLYSALAALADD4 - 3566 - 358

NCS ensembles :
ID
1
2
3
4
5
6

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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-KAS / 3-(1-{[hydroxy(phosphonooxy)boranyl]methyl}-1H-1,2,3-triazol-4-yl)benzoic acid


Mass: 326.995 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H11BN3O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
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: 1.07818 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07818 Å / Relative weight: 1
ReflectionResolution: 1.957→98.88 Å / Num. obs: 96293 / % possible obs: 94.6 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.029 / Rrim(I) all: 0.058 / Net I/σ(I): 13.3
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
1.957-1.96440.41539259880.9290.2350.4792.198.9
9.082-98.8773.50.029358210150.9980.0180.03428.593.5

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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: 4U0T

4u0t


Resolution: 1.96→98.88 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.421 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.18
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 4890 5.1 %RANDOM
Rwork0.2194 ---
obs0.221 91370 94.52 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 110.9 Å2 / Biso mean: 40.318 Å2 / Biso min: 12.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.69 Å2
2---2.45 Å20 Å2
3---0.89 Å2
Refinement stepCycle: final / Resolution: 1.96→98.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11004 0 88 339 11431
Biso mean--58.37 38.45 -
Num. residues----1424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01311380
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710143
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.66415531
X-RAY DIFFRACTIONr_angle_other_deg1.2851.57323631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90451422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71225.029515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.512151795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6211522
X-RAY DIFFRACTIONr_chiral_restr0.0620.21501
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022187
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A112970.07
12B112970.07
21A114460.08
22C114460.08
31A114650.08
32D114650.08
41B110160.08
42C110160.08
51B112550.07
52D112550.07
61C111840.09
62D111840.09
LS refinement shellResolution: 1.96→2.008 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.313 351 -
Rwork0.282 7120 -
obs--99.23 %

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