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- PDB-5w13: ADC-7 in complex with boronic acid transition state inhibitor SM23 -

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Basic information

Entry
Database: PDB / ID: 5w13
TitleADC-7 in complex with boronic acid transition state inhibitor SM23
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / Beta-lactamase / BATSI / ADC-7 / HYDROLASE-HYDROLASE INHIBITOR complex
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-SM2 / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSmolen, K.A. / 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: 2018
Title: Inhibition of Acinetobacter-Derived Cephalosporinase: Exploring the Carboxylate Recognition Site Using Novel beta-Lactamase Inhibitors.
Authors: Caselli, E. / Romagnoli, C. / Powers, R.A. / Taracila, M.A. / Bouza, A.A. / Swanson, H.C. / Smolen, K.A. / Fini, F. / Wallar, B.J. / Bonomo, R.A. / Prati, F.
History
DepositionJun 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)164,5118
Polymers163,2344
Non-polymers1,2774
Water11,295627
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1282
Polymers40,8081
Non-polymers3191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1282
Polymers40,8081
Non-polymers3191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1282
Polymers40,8081
Non-polymers3191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1282
Polymers40,8081
Non-polymers3191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.712, 81.651, 106.415
Angle α, β, γ (deg.)90.00, 112.84, 90.00
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DRA1, beta-lactamase
#2: Chemical
ChemComp-SM2 / (1R)-1-(2-THIENYLACETYLAMINO)-1-(3-CARBOXYPHENYL)METHYLBORONIC ACID


Mass: 319.141 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H14BNO5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.47 %
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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→98.073 Å / Num. obs: 101377 / % possible obs: 99.6 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 1.95→1.96 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 973 / CC1/2: 0.719 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0T

4u0t


Resolution: 1.95→98.07 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.135 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24619 4995 4.9 %RANDOM
Rwork0.18708 ---
obs0.18998 96260 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20.99 Å2
2---2 Å20 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.95→98.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11177 0 88 628 11893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211572
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210431
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.97315753
X-RAY DIFFRACTIONr_angle_other_deg1.109324363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07451424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59725.789513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61151905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1681524
X-RAY DIFFRACTIONr_chiral_restr0.1470.21731
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112868
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022199
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_it2.9243.5175705
X-RAY DIFFRACTIONr_mcbond_other2.9243.5165704
X-RAY DIFFRACTIONr_mcangle_it3.9545.2597126
X-RAY DIFFRACTIONr_mcangle_other3.9545.2597127
X-RAY DIFFRACTIONr_scbond_it3.3813.835867
X-RAY DIFFRACTIONr_scbond_other3.383.835866
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9425.6278628
X-RAY DIFFRACTIONr_long_range_B_refined6.2341.82612776
X-RAY DIFFRACTIONr_long_range_B_other6.21141.76512710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 347 -
Rwork0.27 7167 -
obs--99.62 %

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