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- PDB-5k6d: Structure of FS50 an antagonist of NaV1.5 -

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Basic information

Entry
Database: PDB / ID: 5k6d
TitleStructure of FS50 an antagonist of NaV1.5
ComponentsPutative secreted salivary protein
KeywordsUNKNOWN FUNCTION / flea / xenopsylla / sodium channel
Function / homologyPutative secreted salivary protein
Function and homology information
Biological speciesXenopsylla cheopis (oriental rat flea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.139 Å
AuthorsAndersen, J.F. / Xu, X.
CitationJournal: Sci Rep / Year: 2016
Title: Structure and Function of FS50, a salivary protein from the flea Xenopsylla cheopis that blocks the sodium channel NaV1.5.
Authors: Xu, X. / Zhang, B. / Yang, S. / An, S. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative secreted salivary protein
B: Putative secreted salivary protein


Theoretical massNumber of molelcules
Total (without water)16,4352
Polymers16,4352
Non-polymers00
Water3,063170
1
A: Putative secreted salivary protein


Theoretical massNumber of molelcules
Total (without water)8,2171
Polymers8,2171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative secreted salivary protein


Theoretical massNumber of molelcules
Total (without water)8,2171
Polymers8,2171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.251, 66.627, 42.285
Angle α, β, γ (deg.)90.000, 121.690, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative secreted salivary protein


Mass: 8217.302 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopsylla cheopis (oriental rat flea) / Plasmid: pET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: A2IAD2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 6000, 0.1 M bicine, pH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.96862 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.139→50 Å / Num. obs: 51089 / % possible obs: 98.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 8.62 Å2 / Rmerge(I) obs: 0.038 / Net I/av σ(I): 32.792 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.14-1.162.70.279193.9
1.16-1.183.30.276197.1
1.18-1.23.40.247197.5
1.2-1.233.60.218197.9
1.23-1.253.60.193198.2
1.25-1.283.70.181198.3
1.28-1.323.70.156198.4
1.32-1.353.70.135198.8
1.35-1.393.70.119198.8
1.39-1.443.70.098199
1.44-1.493.70.078199.3
1.49-1.553.70.064199.4
1.55-1.623.70.057199.6
1.62-1.73.80.051199.8
1.7-1.813.80.051199.8
1.81-1.953.70.048199.9
1.95-2.153.80.041199.9
2.15-2.463.80.0311100
2.46-3.093.80.0231100
3.09-223.80.018198.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.139→22.053 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.45
RfactorNum. reflection% reflection
Rfree0.1739 2608 5.11 %
Rwork0.1673 --
obs0.1677 51086 98.61 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 43.82 Å2 / Biso mean: 13.9336 Å2 / Biso min: 5.19 Å2
Refinement stepCycle: final / Resolution: 1.139→22.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 0 170 1293
Biso mean---22.24 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061171
X-RAY DIFFRACTIONf_angle_d1.0651542
X-RAY DIFFRACTIONf_chiral_restr0.045151
X-RAY DIFFRACTIONf_plane_restr0.005205
X-RAY DIFFRACTIONf_dihedral_angle_d13.156453
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1394-1.16010.19331250.22172398252392
1.1601-1.18240.20961360.20242509264597
1.1824-1.20660.20831270.18532501262898
1.2066-1.23280.20991370.18272512264998
1.2328-1.26150.20251400.17022512265298
1.2615-1.2930.19311380.17312546268498
1.293-1.3280.17961440.16892540268499
1.328-1.36710.18021240.16582571269599
1.3671-1.41120.17871290.16562569269899
1.4112-1.46160.17341430.15752565270899
1.4616-1.52010.16081500.14482509265999
1.5201-1.58930.15591410.14452583272499
1.5893-1.6730.17341180.146125992717100
1.673-1.77780.15391400.156825842724100
1.7778-1.9150.16451470.166625852732100
1.915-2.10760.15191230.164725922715100
2.1076-2.41220.19151580.167925732731100
2.4122-3.03790.17251380.18826192757100
3.0379-22.05710.16731500.16242611276199
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)
11.6005-0.82590.14321.6722-1.20741.3727-0.1436-0.32240.13770.27850.1786-0.0477-0.4742-0.4152-0.00090.12970.0625-0.00090.1569-0.00680.0786-28.15084.151518.4925
21.8286-0.5072-0.78173.54641.10772.7476-0.0161-0.0187-0.1266-0.0996-0.017-0.0730.1276-0.00060.02660.05940.0116-0.00290.04740.01350.0519-20.5612-6.686511.6308
33.5123-1.03410.12155.3605-1.32544.61930.26270.0206-0.2934-0.1002-0.0389-0.01120.8487-0.0321-0.17810.167-0.0192-0.02170.06660.02640.1061-22.8982-13.789421.0284
43.30755.02971.43588.80042.95724.01760.1153-0.26440.08230.2061-0.056-0.3231-0.19210.33110.0190.0799-0.0017-0.01230.12510.00530.1055-18.6088-2.297719.9435
55.36340.15491.03144.49871.80046.3102-0.1749-0.2870.24060.3160.1579-0.1331-0.3883-0.00330.00640.1447-0.0118-0.01460.05510.00690.1-19.928911.83722.7235
62.9513-2.49421.21474.3307-1.37682.0096-0.07890.12090.2290.0286-0.0008-0.1039-0.20140.09530.07070.0711-0.0088-0.00120.07670.01080.0866-15.30395.0119-1.5785
73.5089-2.09130.23253.5459-0.14021.9516-0.01820.0939-0.06520.0392-0.0022-0.020.11050.04330.00910.0354-0.00390.00610.042-0.00040.0362-18.5441-2.65641.8489
83.3497-0.7735-3.51057.93151.42777.4986-0.03280.2981-0.0122-0.08170.0226-0.05450.14830.1752-0.00010.02390.00780.01660.13260.01870.0834-9.8894-1.3193-8.6862
92.1501-1.4858-0.42021.8706-0.06131.11280.01130.3895-0.181-0.1077-0.05390.0229-0.0259-0.07580.04720.0485-0.0002-0.00070.0979-0.00340.0553-21.15121.2285-5.0157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:24)A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resseq 25:59)A25 - 59
3X-RAY DIFFRACTION3chain 'A' and (resseq 60:71)A60 - 71
4X-RAY DIFFRACTION4chain 'A' and (resseq 72:77)A72 - 77
5X-RAY DIFFRACTION5chain 'B' and (resseq 0:15)B0 - 15
6X-RAY DIFFRACTION6chain 'B' and (resseq 16:36)B16 - 36
7X-RAY DIFFRACTION7chain 'B' and (resseq 37:59)B37 - 59
8X-RAY DIFFRACTION8chain 'B' and (resseq 60:71)B60 - 71
9X-RAY DIFFRACTION9chain 'B' and (resseq 72:77)B72 - 77

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