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- PDB-8fqn: apo ADC-33 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 8fqn
Titleapo ADC-33 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / Acinetobacter-derived Cephalosporinase / Beta-lactamase
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/transpeptidase-like
Similarity search - Domain/homology
GLYCINE / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.256 Å
AuthorsPowers, R.A. / Wallar, B.J. / June, C.M. / Fish, E.R.
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)82,0847
Polymers81,6292
Non-polymers4555
Water12,881715
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0043
Polymers40,8151
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0804
Polymers40,8151
Non-polymers2653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.116, 83.551, 205.593
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: 40814.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ampC, BAA1790NC_1053, EP550_05490, EP560_12590, EQH48_05445
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7Y407, beta-lactamase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ADC-33 (3.5 mg/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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.256→77.403 Å / Num. obs: 145620 / % possible obs: 91.1 % / Redundancy: 13.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.034 / Net I/σ(I): 12.2
Reflection shellResolution: 1.256→1.365 Å / Rmerge(I) obs: 1.672 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7274 / CC1/2: 0.336 / Rpim(I) all: 0.453 / % possible all: 55.6

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXv1.19.2refinement
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0X

4u0x


Resolution: 1.256→35.67 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 7334 5.04 %
Rwork0.1743 --
obs0.1758 145620 70.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.256→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5620 0 25 715 6360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095906
X-RAY DIFFRACTIONf_angle_d1.058043
X-RAY DIFFRACTIONf_dihedral_angle_d13.4572201
X-RAY DIFFRACTIONf_chiral_restr0.092883
X-RAY DIFFRACTIONf_plane_restr0.0081048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.256-1.260.3463150.3074326X-RAY DIFFRACTION5
1.26-1.280.2797360.3033458X-RAY DIFFRACTION7
1.28-1.290.2967280.2847686X-RAY DIFFRACTION11
1.29-1.310.3008560.2871967X-RAY DIFFRACTION15
1.31-1.330.3113620.26731177X-RAY DIFFRACTION18
1.33-1.340.3597780.291388X-RAY DIFFRACTION21
1.34-1.360.29951160.26211831X-RAY DIFFRACTION29
1.36-1.380.31771260.26692463X-RAY DIFFRACTION38
1.38-1.410.27191770.25813056X-RAY DIFFRACTION47
1.41-1.430.27131820.25263614X-RAY DIFFRACTION55
1.43-1.450.2742190.23934048X-RAY DIFFRACTION63
1.45-1.480.26832410.23674666X-RAY DIFFRACTION71
1.48-1.510.26462750.23975309X-RAY DIFFRACTION82
1.51-1.540.23763340.23245958X-RAY DIFFRACTION91
1.54-1.570.2833200.24056085X-RAY DIFFRACTION95
1.57-1.610.2713500.23816328X-RAY DIFFRACTION97
1.61-1.650.2453480.21426256X-RAY DIFFRACTION96
1.65-1.690.21652900.19555951X-RAY DIFFRACTION91
1.69-1.740.23193280.19436228X-RAY DIFFRACTION95
1.74-1.80.21983080.18766361X-RAY DIFFRACTION97
1.8-1.860.21383290.18276403X-RAY DIFFRACTION98
1.86-1.940.20943530.18186432X-RAY DIFFRACTION98
1.94-2.030.20373640.17136425X-RAY DIFFRACTION98
2.03-2.130.20283780.166454X-RAY DIFFRACTION98
2.13-2.270.20253130.15046525X-RAY DIFFRACTION98
2.27-2.440.18813430.16396495X-RAY DIFFRACTION99
2.44-2.690.19043280.16996634X-RAY DIFFRACTION99
2.69-3.080.20082920.17596178X-RAY DIFFRACTION92
3.08-3.880.18793670.15316600X-RAY DIFFRACTION98
3.88-35.670.16693780.13896984X-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)
10.7180.2948-0.12911.3844-0.24680.8161-0.0286-0.1183-0.05650.0839-0.0115-0.03420.0611-0.03240.03850.08080.01820.0090.0881-0.00830.066434.19911.669-36.908
20.4253-0.86520.15381.933-0.38370.1287-0.0263-0.2075-0.10360.14890.1010.1859-0.0108-0.0739-0.10770.14260.01230.02080.1536-0.00260.100929.01724.765-34.924
30.35910.34940.01541.62090.13780.6717-0.0248-0.0138-0.0468-0.06540.017-0.05440.01930.02350.01240.05720.00770.01840.0608-0.00030.068138.6488.908-48.319
41.32610.2027-0.4930.9804-0.6381.53380.0150.2166-0.0489-0.06130.03840.03290.0974-0.1933-0.0510.0817-0.0073-0.01560.1076-0.01230.041826.2095.142-83.529
52.09850.3423-0.97970.8303-0.49241.63920.14860.0280.24310.2179-0.0189-0.0192-0.2607-0.0126-0.11320.13860.0103-0.00050.10140.00390.073134.72319.45-85.374
60.2043-0.08910.15330.7962-1.2443.03220.01120.05510.06090.1413-0.0564-0.0779-0.23330.08660.03570.1466-0.0197-0.00030.1087-0.01720.102129.6558.274-70.291
71.38450.1997-0.0510.8402-0.26341.23790.01850.558-0.0303-0.11340.01990.01190.0537-0.2753-0.0420.1013-0.0007-0.0080.2388-0.01430.071825.4466.72-94.478
82.35321.96970.35463.70630.1442.0332-0.15860.5084-0.304-0.1792-0.0662-0.3030.29490.13620.10770.1230.03160.05130.2544-0.07150.142540.6891.045-96.288
91.6352-0.0093-0.14052.3008-0.51943.207-0.02020.2513-0.3155-0.149-0.0092-0.11590.3393-0.038-0.03510.1133-0.01530.00780.1203-0.04730.084130.005-3.7-86.336
104.5456-4.926-3.61379.14437.24275.82911.2414-1.55281.49415.1581.8273-1.246-1.8007-5.6556-3.06880.4607-0.25640.02170.5699-0.08910.585219.153-15.686-95.274
112.13861.99231.98321.96231.98662.0211-0.4064-2.205-1.15982.57350.5281-1.0183-3.84977.1594-0.13030.4115-0.0673-0.08460.51490.02820.471638.1561.363-87.822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:192 )B1 - 192
2X-RAY DIFFRACTION2( CHAIN B AND RESID 193:225 )B193 - 225
3X-RAY DIFFRACTION3( CHAIN B AND RESID 226:360 )B226 - 360
4X-RAY DIFFRACTION4( CHAIN A AND RESID 2:105 )A2 - 105
5X-RAY DIFFRACTION5( CHAIN A AND RESID 106:192 )A106 - 192
6X-RAY DIFFRACTION6( CHAIN A AND RESID 193:225 )A193 - 225
7X-RAY DIFFRACTION7( CHAIN A AND RESID 226:276 )A226 - 276
8X-RAY DIFFRACTION8( CHAIN A AND RESID 277:308 )A277 - 308
9X-RAY DIFFRACTION9( CHAIN A AND RESID 309:358 )A309 - 358
10X-RAY DIFFRACTION10( CHAIN A AND RESID 359:359 )A359
11X-RAY DIFFRACTION11( CHAIN A AND RESID 402:402 )A402

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