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- PDB-6u3t: Structure-based discovery of a novel small-molecule inhibitor of ... -

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Basic information

Entry
Database: PDB / ID: 6u3t
TitleStructure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus
ComponentsAlpha-hemolysinHemolysin
KeywordsTOXIN / alpha-toxin / PVL / Leukocidins / MRSA
Function / homology
Function and homology information


cytolysis in another organism / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
fos-choline-14 / Alpha-hemolysin
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsLiu, J. / Kozhaya, L. / Torres, V.J. / Unutmaz, D. / Lu, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure-based discovery of a small-molecule inhibitor of methicillin-resistantStaphylococcus aureusvirulence.
Authors: Liu, J. / Kozhaya, L. / Torres, V.J. / Unutmaz, D. / Lu, M.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-hemolysin
B: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,54412
Polymers66,4462
Non-polymers2,09810
Water91951
1
A: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1765
Polymers33,2231
Non-polymers9534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3687
Polymers33,2231
Non-polymers1,1456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Alpha-hemolysin
B: Alpha-hemolysin
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)548,35596
Polymers531,56716
Non-polymers16,78880
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
crystal symmetry operation5_755-x+2,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area46500 Å2
ΔGint-597 kcal/mol
Surface area160550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.180, 136.180, 166.045
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-406-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 18 - 292 / Label seq-ID: 18 - 292

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alpha-hemolysin / Hemolysin / Alpha-HL / Alpha-toxin


Mass: 33222.930 Da / Num. of mol.: 2 / Fragment: UNP residues 27-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: hly, hla / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P09616
#2: Chemical
ChemComp-PQJ / fos-choline-14 / tetradecyl 2-(trimethyl-$l^{4}-azanyl)ethyl hydrogen phosphate


Mass: 380.523 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H43NO4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10 mg/mL protein in 10 mM sodium acetate, pH 5.4, 5 mM Fos-Choline-14, 40 mM beta-OG, 0.4 mM Deoxy-Big CHAP against reservoir solution of 1.5 M ammonium sulfate, 0.25 M potassium sodium ...Details: 10 mg/mL protein in 10 mM sodium acetate, pH 5.4, 5 mM Fos-Choline-14, 40 mM beta-OG, 0.4 mM Deoxy-Big CHAP against reservoir solution of 1.5 M ammonium sulfate, 0.25 M potassium sodium tartrate, 0.1 M sodium citrate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.79→43.82 Å / Num. obs: 19666 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.956 / Rmerge(I) obs: 0.135 / Net I/σ(I): 5.4
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1262 / CC1/2: 0.716 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4YHD

4yhd


Resolution: 2.79→43.82 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.885 / SU B: 26.349 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.877 / ESU R Free: 0.333 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 975 5 %RANDOM
Rwork0.1971 ---
obs0.1996 18691 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 167.11 Å2 / Biso mean: 71.638 Å2 / Biso min: 48.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-0 Å2
2---0.76 Å20 Å2
3---1.52 Å2
Refinement stepCycle: final / Resolution: 2.79→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 75 51 4240
Biso mean--116.12 59.38 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124275
X-RAY DIFFRACTIONr_angle_refined_deg0.9561.6615792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80123.624229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28815754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9541520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023230
Refine LS restraints NCS

Ens-ID: 1 / Number: 8316 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.79→2.862 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 66 -
Rwork0.295 1268 -
all-1334 -
obs--93.29 %
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)
18.6047-8.4378-10.176612.087611.568413.6267-0.2899-0.8275-0.3757-0.14310.09940.4802-0.24670.96340.19050.2791-0.04140.05960.3065-0.03590.2152146.119-32.38454.534
23.4553-1.6298-2.84390.77141.32423.0145-0.3012-0.0579-0.26660.15510.03030.12150.36020.05230.27090.15520.02730.04020.1824-0.01050.1954144.739-34.4950.507
33.1-0.767-3.38030.27731.02394.2603-0.07-0.1445-0.06380.13680.0748-0.03080.31740.1584-0.00480.20810.03790.0010.136-0.00580.1614143.319-34.60243.01
43.76250.1814-3.25430.0128-0.16433.0125-0.5391-0.0445-0.5023-0.03760.056-0.02590.75890.07930.48320.44350.0690.07320.2116-0.04610.2054147.389-41.98328.876
50.70941.3741-1.79355.0286-6.63348.75190.0447-0.0139-0.1831-0.15180.00860.03290.2011-0.0174-0.05330.1516-0.00350.04250.1643-0.03040.1997130.037-34.94146.042
60.7783-2.5636-1.88898.80018.576820.71620.02540.05150.0891-0.1056-0.2719-0.1972-0.099-0.77780.24660.03110.0347-0.02720.10180.00560.1128137.924-21.52237.986
74.6894-4.71173.288712.85921.899313.2145-0.0397-0.03190.10820.57950.1786-0.3108-0.04090.2596-0.13880.1474-0.0262-0.00670.09520.0340.1059141.03-22.89243.375
84.86580.3656-1.06360.04740.21876.27890.0050.21990.0141-0.00510.04520.01550.1937-0.1811-0.05020.18570.0242-0.02990.19730.05340.1219139.311-30.60530.986
96.1023.9125-8.03123.7265-6.176711.8964-0.15170.16640.2231-0.42420.22440.190.6613-0.242-0.07270.18350.02440.060.20530.01850.1798135.393-36.11534.969
106.6092-5.2282-0.68876.0168-3.4638.6167-0.17410.15180.17020.3390.007-0.2171-0.4486-0.27940.16710.2269-0.04710.0070.16920.08040.2133148.79-26.26212.955
110.6596-1.5744-0.44415.26772.79042.33830.0095-0.3030.05750.0711-0.0503-0.0120.0168-0.81810.04080.11180.10780.03360.82810.0810.2343141.964-35.54716.095
1211.86416.9732-3.95085.22521.523314.4418-0.38380.0409-0.048-0.4293-0.12550.1131-0.5644-0.55760.50920.07610.101-0.04760.2722-0.04230.0771145.697-38.2415.658
131.03461.1549-2.13749.15050.12065.27680.08480.13430.27840.12510.48840.1942-0.0538-0.0983-0.57320.17760.06270.00870.22820.01340.1434151.701-34.47213.626
141.7753-0.8058-1.90185.9165-1.31652.95770.0713-0.04960.5592-0.09860.3225-0.6703-0.01970.1199-0.39380.14730.00570.04530.5220.00120.3194158.478-33.90815.088
150.33810.0937-1.321.0472-0.43365.17570.12680.00740.05060.05690.10640.0129-0.4565-0.016-0.23320.23440.0307-0.00960.1860.04620.1702141.238-32.19442.317
162.76270.1429-3.95320.1153-0.24766.5878-0.1948-0.0006-0.33150.0225-0.08510.02060.33570.0190.27980.1510.01750.01330.11680.01830.1624140.831-41.80743.026
1712.46-1.5098-7.26760.1920.8754.2426-0.14170.4483-0.4297-0.012-0.0710.08540.09-0.26080.21270.19230.0107-0.04560.3015-0.02790.1615154.327-41.8745.873
181.76740.0555-3.11711.5904-0.45245.6968-0.43350.0708-0.25440.0517-0.0277-0.07840.9098-0.18190.46130.2572-0.06780.00420.1238-0.01160.2203144.567-44.7437.771
1914.0109-2.1174-3.71622.0234-1.72168.0324-0.3654-0.8629-0.35640.01780.05750.08760.23030.17020.30790.15240.0152-0.01520.08290.03680.0641140.185-37.62961.867
203.98741.56861.23541.6077-0.50491.41190.14070.75240.03770.25730.15910.3368-0.10070.4984-0.29980.25120.13560.01470.5215-0.02870.2686120.173-27.27256.139
212.4686-1.29610.42390.90670.47752.28990.2188-0.13590.21690.07860.0888-0.24040.5556-0.1638-0.30760.2422-0.04760.01160.1452-0.01670.1997117.995-30.5250.292
220.6283-0.5703-0.85210.73210.82722.0964-0.0985-0.1488-0.12090.12040.04020.09890.19780.25620.05830.1865-0.020.01410.18610.00910.1798117.274-29.61843.026
231.328-1.1832-2.37051.09351.8636.4454-0.10360.2094-0.13720.1004-0.12110.12140.5299-0.64430.22470.2118-0.04560.0340.2115-0.08750.1982115.312-37.7928.858
242.8858-0.4889-3.70690.9023-0.98318.03480.0443-0.10490.06430.040.13310.067-0.278-0.1439-0.17740.1854-0.0384-0.01060.1775-0.06030.14107.238-20.26445.813
251.80311.0514-1.20232.55911.568517.9914-0.15310.0125-0.1216-0.07780.115-0.0225-0.48990.46970.03810.0639-0.02490.02140.0429-0.01910.1467122.248-16.33737.939
269.44345.0704-4.51396.88171.86718.00110.2377-0.26790.15380.3319-0.1627-0.20610.15950.1838-0.0750.13940.02820.00910.05570.05130.3158123.525-19.59243.367
2712.1085-2.2211-0.70742.97311.02330.353-0.07140.09120.14860.04910.00140.18080.0178-0.01110.07010.15520.0076-0.00220.20410.05860.0764117.105-23.83330.72
285.8092-0.5534-6.51590.4670.25938.9634-0.03660.11440.04540.04770.0317-0.01740.0496-0.14120.00490.1029-0.0459-0.02170.0959-0.01750.1599110.581-24.98834.577
2918.1629-5.1196-7.998110.897812.89115.4889-0.44480.94660.5839-0.56480.6108-0.0953-0.5820.5615-0.1660.1193-0.08450.03830.1798-0.00710.2142127.937-27.82513.236
305.60371.161-6.34214.43513.069111.7633-0.4464-0.109-0.2447-0.62430.00240.1132-0.04690.11610.4440.1106-0.0189-0.00890.2528-0.0310.1049116.426-29.77815.697
3124.9416-20.5459-6.117721.88988.97594.62260.06690.4935-0.3563-0.2599-0.31690.4988-0.1751-0.06290.250.1011-0.06540.0050.1737-0.01070.0301117.92-34.75.469
320.4339-2.2173-0.147512.44341.17670.22310.11920.1043-0.0953-0.66330.01550.09030.02770.1892-0.13470.31370.0916-0.03590.4269-0.14210.2251124.348-35.83213.861
332.35571.15560.37440.6634-0.61398.43680.28370.1973-0.38510.07020.0646-0.23430.1490.5513-0.34830.21130.09550.15590.4228-0.06920.336129.513-40.21315.918
345.423-3.4019-7.48432.28744.215412.1330.07160.20780.0541-0.0418-0.1528-0.0187-0.0596-0.24680.08120.0709-0.06190.01690.099-0.03020.1458117.362-26.14542.251
352.0813-1.3999-4.47491.71214.306912.2996-0.24790.0183-0.25820.1135-0.21640.23230.3761-0.1940.46440.1465-0.0130.01610.1519-0.04140.1681110.415-32.89142.753
363.6464-3.1396-2.01716.73.86092.5816-0.13880.0406-0.22-0.3099-0.38780.57930.1097-0.27010.52660.3037-0.00510.08650.1868-0.10410.1893121.61-43.2386.141
371.4160.0681-1.64280.84191.68085.6899-0.12610.0608-0.12480.089-0.0445-0.02080.219-0.130.17060.2172-0.016-0.01750.05970.01310.204111.033-37.7837.118
382.6975-3.2391.3957.21533.92110.3585-0.1681-0.132-0.00860.43980.0429-0.01240.2922-0.19590.12520.0983-0.04170.01690.07650.02640.1447112.41-29.42561.492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 29
2X-RAY DIFFRACTION2A30 - 45
3X-RAY DIFFRACTION3A46 - 70
4X-RAY DIFFRACTION4A71 - 91
5X-RAY DIFFRACTION5A92 - 107
6X-RAY DIFFRACTION6A108 - 117
7X-RAY DIFFRACTION7A143 - 148
8X-RAY DIFFRACTION8A149 - 158
9X-RAY DIFFRACTION9A159 - 174
10X-RAY DIFFRACTION10A175 - 181
11X-RAY DIFFRACTION11A182 - 186
12X-RAY DIFFRACTION12A187 - 192
13X-RAY DIFFRACTION13A193 - 199
14X-RAY DIFFRACTION14A200 - 217
15X-RAY DIFFRACTION15A218 - 235
16X-RAY DIFFRACTION16A236 - 258
17X-RAY DIFFRACTION17A259 - 268
18X-RAY DIFFRACTION18A269 - 284
19X-RAY DIFFRACTION19A285 - 293
20X-RAY DIFFRACTION20B16 - 29
21X-RAY DIFFRACTION21B30 - 45
22X-RAY DIFFRACTION22B46 - 70
23X-RAY DIFFRACTION23B71 - 91
24X-RAY DIFFRACTION24B92 - 107
25X-RAY DIFFRACTION25B108 - 117
26X-RAY DIFFRACTION26B143 - 148
27X-RAY DIFFRACTION27B149 - 158
28X-RAY DIFFRACTION28B159 - 174
29X-RAY DIFFRACTION29B175 - 181
30X-RAY DIFFRACTION30B182 - 186
31X-RAY DIFFRACTION31B187 - 192
32X-RAY DIFFRACTION32B193 - 199
33X-RAY DIFFRACTION33B200 - 217
34X-RAY DIFFRACTION34B218 - 235
35X-RAY DIFFRACTION35B236 - 258
36X-RAY DIFFRACTION36B259 - 268
37X-RAY DIFFRACTION37B269 - 284
38X-RAY DIFFRACTION38B285 - 293

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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