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- PDB-8fqr: Apo ADC-212 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 8fqr
TitleApo ADC-212 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / Acinetobacter-derived cephalosporinase
Function / homologyGLYCINE / PHOSPHATE ION
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsPowers, R.A. / Wallar, B.J. / June, C.M. / Beardsley, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI072219 United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter -Derived Cephalosporinase Variants with an Expanded-Substrate Spectrum.
Authors: Powers, R.A. / June, C.M. / Fernando, M.C. / Fish, E.R. / Maurer, O.L. / Baumann, R.M. / Beardsley, T.J. / Taracila, M.A. / Rudin, S.D. / Hujer, K.M. / Hujer, A.M. / Santi, N. / Villamil, V. ...Authors: Powers, R.A. / June, C.M. / Fernando, M.C. / Fish, E.R. / Maurer, O.L. / Baumann, R.M. / Beardsley, T.J. / Taracila, M.A. / Rudin, S.D. / Hujer, K.M. / Hujer, A.M. / Santi, N. / Villamil, V. / Introvigne, M.L. / Prati, F. / Caselli, E. / Bonomo, R.A. / Wallar, B.J.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9853
Polymers40,8151
Non-polymers1702
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: monomeric biological assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.388, 69.805, 55.124
Angle α, β, γ (deg.)90.00, 114.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 40814.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ampC / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#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.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 42.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M SPG, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.24→49.98 Å / Num. obs: 83353 / % possible obs: 87.4 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.018 / Rrim(I) all: 0.034 / Χ2: 0.79 / Net I/σ(I): 18 / Num. measured all: 297334
Reflection shellResolution: 1.24→1.31 Å / % possible obs: 83.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.455 / Num. measured all: 40509 / Num. unique obs: 11584 / CC1/2: 0.82 / Rpim(I) all: 0.285 / Rrim(I) all: 0.539 / Χ2: 0.6 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIXv1.19refinement
Cootmodel building
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0X

4u0x


Resolution: 1.24→49.98 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 4203 5.04 %
Rwork0.1583 --
obs0.1592 83325 87.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 10 360 3168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073020
X-RAY DIFFRACTIONf_angle_d0.9614118
X-RAY DIFFRACTIONf_dihedral_angle_d12.5271146
X-RAY DIFFRACTIONf_chiral_restr0.093448
X-RAY DIFFRACTIONf_plane_restr0.008542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.27371510.25882816X-RAY DIFFRACTION99
1.27-1.290.25481470.22713014X-RAY DIFFRACTION100
1.29-1.30.23081360.21593007X-RAY DIFFRACTION100
1.3-1.320.21121540.21253027X-RAY DIFFRACTION100
1.32-1.340.23321650.20523008X-RAY DIFFRACTION100
1.34-1.360.23931720.21322991X-RAY DIFFRACTION100
1.36-1.380.2365750.22641350X-RAY DIFFRACTION45
1.38-1.40.21441630.19272959X-RAY DIFFRACTION100
1.4-1.420.22591590.19113006X-RAY DIFFRACTION100
1.42-1.450.19431750.17793025X-RAY DIFFRACTION100
1.45-1.470.1911010.17522161X-RAY DIFFRACTION99
1.48-1.50.18731320.1712555X-RAY DIFFRACTION97
1.5-1.530.22911130.16891832X-RAY DIFFRACTION61
1.53-1.570.14911640.15893012X-RAY DIFFRACTION100
1.57-1.60.16891610.15422981X-RAY DIFFRACTION100
1.6-1.640.17771690.15632985X-RAY DIFFRACTION100
1.64-1.690.17921460.15433019X-RAY DIFFRACTION100
1.69-1.740.18481670.15613007X-RAY DIFFRACTION100
1.74-1.790.18651570.15913027X-RAY DIFFRACTION100
1.79-1.860.1831730.15982980X-RAY DIFFRACTION100
1.86-1.930.1847770.16121387X-RAY DIFFRACTION46
1.93-2.020.1852990.15392092X-RAY DIFFRACTION69
2.02-2.120.15881180.15062255X-RAY DIFFRACTION74
2.12-2.220.16391210.14712298X-RAY DIFFRACTION100
2.26-2.430.2021530.15522896X-RAY DIFFRACTION98
2.43-2.640.18851440.16312671X-RAY DIFFRACTION99
2.68-3.060.19081610.1622905X-RAY DIFFRACTION99
3.06-3.860.14441710.14752881X-RAY DIFFRACTION95
3.86-49.980.15171310.13682963X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.68520.07720.4442.3462-0.11231.9812-0.0259-0.0619-0.0870.1270.07590.07650.1638-0.1581-0.02990.1331-0.0035-0.00410.09420.02180.10863.2478-32.653718.2133
21.20830.09950.19211.8965-0.83941.5724-0.03540.10540.0603-0.1605-0.0098-0.0906-0.00170.1390.03250.10850.00670.0150.1086-0.00770.106119.851-4.18686.7485
30.92760.5796-0.00922.17030.73151.1832-0.01480.0947-0.0779-0.02930.0855-0.18070.04490.0928-0.07160.12560.0298-0.00820.13380.0010.146917.7293-21.39216.3817
41.43480.50610.05761.8191-0.84751.9819-0.03310.00680.10690.0240.08630.4067-0.2067-0.2093-0.05380.15540.05420.00560.15940.02590.2160.4277-5.380213.3947
51.62830.15330.3562.83990.02871.2957-0.02210.01090.10170.04880.07910.2214-0.017-0.2216-0.04160.08580.00550.0070.11270.02210.11040.7499-20.41816.1033
62.0001-1.0212.00012.000122.00012.58363.40845.1873-0.8625-1.2515-0.4759-3.3855-0.1242-1.31810.43210.2643-0.01090.55420.02530.59048.8839-8.176929.2695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 5 through 62 )
2X-RAY DIFFRACTION2chain 'B' and (resid 63 through 166 )
3X-RAY DIFFRACTION3chain 'B' and (resid 167 through 257 )
4X-RAY DIFFRACTION4chain 'B' and (resid 258 through 308 )
5X-RAY DIFFRACTION5chain 'B' and (resid 309 through 359 )
6X-RAY DIFFRACTION6chain 'B' and (resid 401 through 401 )

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