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- PDB-8fqt: Apo ADC-219 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 8fqt
TitleApo ADC-219 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / Acinetobacter-derived cephalosporinase
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsPowers, R.A. / Wallar, B.J. / June, C.M. / Maurer, O.L.
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
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9354
Polymers81,7452
Non-polymers1902
Water6,648369
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9682
Polymers40,8731
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9682
Polymers40,8731
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.041, 83.567, 206.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 40872.590 Da / Num. of mol.: 2
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
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-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.89→77.46 Å / Num. obs: 59691 / % possible obs: 98.1 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rpim(I) all: 0.043 / Net I/σ(I): 9.6
Reflection shellResolution: 1.89→1.9 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 608 / CC1/2: 0.885 / Rpim(I) all: 0.303 / % possible all: 100

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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: 1.89→40.95 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2415 1998 3.35 %
Rwork0.1964 --
obs0.1979 59650 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5521 0 10 369 5900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065692
X-RAY DIFFRACTIONf_angle_d0.7917735
X-RAY DIFFRACTIONf_dihedral_angle_d14.2672105
X-RAY DIFFRACTIONf_chiral_restr0.051854
X-RAY DIFFRACTIONf_plane_restr0.0061005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.34571430.2594143X-RAY DIFFRACTION100
1.94-1.990.271420.23924114X-RAY DIFFRACTION100
1.99-2.050.32811440.23694132X-RAY DIFFRACTION99
2.05-2.110.26691170.22713390X-RAY DIFFRACTION83
2.11-2.190.25531420.21934089X-RAY DIFFRACTION98
2.19-2.280.28211440.21844155X-RAY DIFFRACTION100
2.28-2.380.27791450.22984149X-RAY DIFFRACTION100
2.38-2.510.2941430.23274135X-RAY DIFFRACTION100
2.51-2.660.30931440.2314176X-RAY DIFFRACTION99
2.66-2.870.2971460.22854182X-RAY DIFFRACTION99
2.87-3.160.25541440.20864147X-RAY DIFFRACTION99
3.16-3.610.23291460.19374228X-RAY DIFFRACTION99
3.61-4.550.1721440.14994130X-RAY DIFFRACTION97
4.55-40.950.19831540.16384482X-RAY DIFFRACTION99
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)
11.46140.4932-0.39662.0302-0.26941.6063-0.0355-0.1740.0510.0765-0.0541-0.13160.06730.02910.07940.23080.01570.02320.1771-0.03130.1587-4.82116.753-41.939
22.738-0.5260.90732.3445-0.51274.7377-0.089-0.3122-0.08880.4127-0.10520.33320.2127-0.70150.22370.3752-0.02490.1130.338-0.01510.3097-18.9742.064-33.767
31.4284-1.40410.5172.5162-0.49741.408-0.1394-0.25950.08130.39050.16810.0269-0.0956-0.1155-0.05540.304-0.01060.04520.2271-0.01770.2074-5.34420.574-33.961
40.49930.2335-0.13642.24090.25811.2485-0.04370.0049-0.0644-0.0775-0.00780.01320.0940.03670.0520.25440.01310.04660.21930.00470.2522-5.1788.517-49.664
51.43690.4702-0.60742.4142-1.45222.5535-0.06720.2242-0.2864-0.13070.05930.00710.3708-0.25620.02720.2299-0.04930.00250.2746-0.01670.2467-19.948-2.937-80.101
64.0238-0.3663-0.91923.58710.13090.93970.11160.06370.34340.25450.0452-0.136-0.24110.0045-0.1490.2918-0.0149-0.00020.31390.01890.1861-3.86423.649-89.444
70.5569-0.09990.080.7566-0.91952.99680.05210.0840.16590.07780.07210.0186-0.1432-0.2787-0.10450.278-0.00140.04070.29820.02950.2587-20.06510.34-77.617
83.1637-0.1897-1.1131.5470.02681.3125-0.05570.4831-0.0533-0.1112-0.024-0.14650.1131-0.02920.0790.2447-0.03050.01390.3693-0.01220.1629-9.6735.126-97.181
92.9605-0.2561-1.45853.0748-0.89075.25830.01920.3257-0.3242-0.21550.1287-0.08110.26320.0624-0.14460.2406-0.00990.01030.2476-0.02550.2232-13.479-3.74-87.115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:104 )B1 - 104
2X-RAY DIFFRACTION2( CHAIN B AND RESID 105:165 )B105 - 165
3X-RAY DIFFRACTION3( CHAIN B AND RESID 166:239 )B166 - 239
4X-RAY DIFFRACTION4( CHAIN B AND RESID 240:359 )B240 - 359
5X-RAY DIFFRACTION5( CHAIN A AND RESID 2:78 )A2 - 78
6X-RAY DIFFRACTION6( CHAIN A AND RESID 79:165 )A79 - 165
7X-RAY DIFFRACTION7( CHAIN A AND RESID 166:239 )A166 - 239
8X-RAY DIFFRACTION8( CHAIN A AND RESID 240:307 )A240 - 307
9X-RAY DIFFRACTION9( CHAIN A AND RESID 308:359 )A308 - 359

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