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- PDB-5w12: ADC-7 in complex with boronic acid transition state inhibitor EC04 -

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Basic information

Entry
Database: PDB / ID: 5w12
TitleADC-7 in complex with boronic acid transition state inhibitor EC04
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / Beta-lactamase / BATSI / EC04 / 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-9TG / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 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)164,5678
Polymers163,2344
Non-polymers1,3334
Water9,296516
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1422
Polymers40,8081
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1422
Polymers40,8081
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1422
Polymers40,8081
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1422
Polymers40,8081
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.526, 81.302, 106.690
Angle α, β, γ (deg.)90.00, 112.89, 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-9TG / 3-[(2R)-2-borono-2-{[(thiophen-2-yl)acetyl]amino}ethyl]benzoic acid / boronic acid transition state inhibitor EC04


Mass: 333.167 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H16BNO5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
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: 1.88→98.285 Å / Num. obs: 113662 / % possible obs: 99 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.7
Reflection shellResolution: 1.88→1.886 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1169 / CC1/2: 0.734 / % possible all: 98.1

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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: 1.88→98.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.708 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25482 5668 5 %RANDOM
Rwork0.20084 ---
obs0.20357 107968 99.02 %-
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: 39.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.94 Å2
2---1.89 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.88→98.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11151 0 92 516 11759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211552
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210496
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.97215715
X-RAY DIFFRACTIONr_angle_other_deg1.094324515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12651425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7925.729501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.297151926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0461523
X-RAY DIFFRACTIONr_chiral_restr0.1170.21729
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112798
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022186
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_it3.4113.8475703
X-RAY DIFFRACTIONr_mcbond_other3.4113.8475702
X-RAY DIFFRACTIONr_mcangle_it4.465.7537127
X-RAY DIFFRACTIONr_mcangle_other4.465.7537128
X-RAY DIFFRACTIONr_scbond_it3.6944.2165849
X-RAY DIFFRACTIONr_scbond_other3.6944.2165850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3186.1898589
X-RAY DIFFRACTIONr_long_range_B_refined6.76145.80612805
X-RAY DIFFRACTIONr_long_range_B_other6.74745.75212733
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 423 -
Rwork0.303 7939 -
obs--98.56 %

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