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- PDB-5wad: ADC-7 in complex with boronic acid transition state inhibitor CR161 -

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Basic information

Entry
Database: PDB / ID: 5wad
TitleADC-7 in complex with boronic acid transition state inhibitor CR161
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / Beta-lactamase / BATSI / ADC-7 / ANTIMICROBIAL PROTEIN / 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
PHOSPHATE ION / Chem-QQZ / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPowers, 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)AI072219 United States
CitationJournal: ACS Infect Dis / Year: 2018
Title: Structure-Based Analysis of Boronic Acids as Inhibitors of Acinetobacter-Derived Cephalosporinase-7, a Unique Class C beta-Lactamase.
Authors: Bouza, A.A. / Swanson, H.C. / Smolen, K.A. / VanDine, A.L. / Taracila, M.A. / Romagnoli, C. / Caselli, E. / Prati, F. / Bonomo, R.A. / Powers, R.A. / Wallar, B.J.
History
DepositionJun 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 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 13, 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)164,7859
Polymers163,2344
Non-polymers1,5515
Water6,666370
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1732
Polymers40,8081
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2683
Polymers40,8081
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1732
Polymers40,8081
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1732
Polymers40,8081
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.268, 81.470, 105.908
Angle α, β, γ (deg.)90.00, 112.50, 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-QQZ / phosphonooxy-[[[6-(1~{H}-1,2,3,4-tetrazol-5-yl)pyridin-3-yl]sulfonylamino]methyl]borinic acid


Mass: 364.040 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H10BN6O7PS
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
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-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.09→97.845 Å / Num. obs: 82578 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.5
Reflection shellResolution: 2.09→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2 / Num. unique obs: 2967 / % possible all: 99.8

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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: 2.09→97.84 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.896 / SU B: 7.204 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 4124 5 %RANDOM
Rwork0.214 ---
obs0.218 78433 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å21.04 Å2
2---2 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.09→97.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10785 0 97 370 11252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211163
X-RAY DIFFRACTIONr_bond_other_d0.0020.029887
X-RAY DIFFRACTIONr_angle_refined_deg1.791.9715228
X-RAY DIFFRACTIONr_angle_other_deg1.081323013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24151399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.72825.539473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.084151731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.81522
X-RAY DIFFRACTIONr_chiral_restr0.1060.21686
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112465
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022137
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_it2.9233.7835620
X-RAY DIFFRACTIONr_mcbond_other2.9223.7825619
X-RAY DIFFRACTIONr_mcangle_it4.2145.6567011
X-RAY DIFFRACTIONr_mcangle_other4.2135.6567012
X-RAY DIFFRACTIONr_scbond_it2.9423.9895543
X-RAY DIFFRACTIONr_scbond_other2.9353.9875537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4245.98209
X-RAY DIFFRACTIONr_long_range_B_refined6.18844.8412311
X-RAY DIFFRACTIONr_long_range_B_other6.17244.82312274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 313 -
Rwork0.293 5755 -
obs--99.8 %

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