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- PDB-6ste: Crystal structure of the tick chemokine-binding protein Evasin-4 ... -

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Basic information

Entry
Database: PDB / ID: 6ste
TitleCrystal structure of the tick chemokine-binding protein Evasin-4 (SG 3)
ComponentsEvasin-4
KeywordsIMMUNE SYSTEM / CHEMOKINE-BINDING PROTEIN / TICKS
Function / homologynegative regulation of chemokine activity / Evasins Class A / Evasins Class A / C-C chemokine binding / Immunoglobulin-like domain / extracellular region / ACETATE ION / DI(HYDROXYETHYL)ETHER / Evasin-4
Function and homology information
Biological speciesRhipicephalus sanguineus (brown dog tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsRamirez-Escudero, M. / Janssen, B.J.C.
Funding support1items
OrganizationGrant numberCountry
European Research Council677500
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural characterization of anti-CCL5 activity of the tick salivary protein evasin-4.
Authors: Denisov, S.S. / Ramirez-Escudero, M. / Heinzmann, A.C.A. / Ippel, J.H. / Dawson, P.E. / Koenen, R.R. / Hackeng, T.M. / Janssen, B.J.C. / Dijkgraaf, I.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: Evasin-4
B: Evasin-4
D: Evasin-4
C: Evasin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,82710
Polymers45,2654
Non-polymers5626
Water4,288238
1
A: Evasin-4
B: Evasin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0296
Polymers22,6332
Non-polymers3964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-13 kcal/mol
Surface area10150 Å2
MethodPISA
2
D: Evasin-4
C: Evasin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7984
Polymers22,6332
Non-polymers1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-9 kcal/mol
Surface area9910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.214, 68.214, 181.531
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 18 or resid 20 through 49...
21(chain C and (resid 18 or resid 20 through 49...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASP(chain A and (resid 18 or resid 20 through 49...AA1818
12THRTHRTHRTHR(chain A and (resid 18 or resid 20 through 49...AA20 - 4920 - 49
13THRTHRPHEPHE(chain A and (resid 18 or resid 20 through 49...AA51 - 6951 - 69
14PROPROARGARG(chain A and (resid 18 or resid 20 through 49...AA81 - 9981 - 99
15ALAALATRPTRP(chain A and (resid 18 or resid 20 through 49...AA101 - 104101 - 104
21ASPASPASPASP(chain C and (resid 18 or resid 20 through 49...CD1818
22THRTHRTHRTHR(chain C and (resid 18 or resid 20 through 49...CD20 - 4920 - 49
23THRTHRPHEPHE(chain C and (resid 18 or resid 20 through 49...CD51 - 6951 - 69
24PROPROARGARG(chain C and (resid 18 or resid 20 through 49...CD81 - 9981 - 99
25ALAALATRPTRP(chain C and (resid 18 or resid 20 through 49...CD101 - 104101 - 104

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Components

#1: Protein
Evasin-4


Mass: 11316.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus sanguineus (brown dog tick)
Production host: Escherichia coli (E. coli) / References: UniProt: P0C8E9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.69 Å3/Da / Density % sol: 61 % / Description: pentagonal prism
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% glycerol, 25.5% PEG 4000, 0.17 M ammonium acetate, 85 mM acetate buffer pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97717 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97717 Å / Relative weight: 1
ReflectionResolution: 1.79→59.07 Å / Num. obs: 47147 / % possible obs: 99.97 % / Redundancy: 19.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.1
Reflection shellResolution: 1.79→1.85 Å / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 3 / Num. unique obs: 3398 / CC1/2: 0.559

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ST4

6st4


Resolution: 1.79→56.175 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 20.35
RfactorNum. reflection% reflection
Rfree0.2096 2360 5.01 %
Rwork0.1793 --
obs0.1808 47078 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.94 Å2 / Biso mean: 38.4992 Å2 / Biso min: 12.72 Å2
Refinement stepCycle: final / Resolution: 1.79→56.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 37 238 2788
Biso mean--46.85 44.66 -
Num. residues----332
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A412X-RAY DIFFRACTION8.155TORSIONAL
12C412X-RAY DIFFRACTION8.155TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.79-1.82630.34761380.2988252099
1.8263-1.8660.28131400.27762575100
1.866-1.90950.28391220.24362630100
1.9095-1.95720.25341180.22172614100
1.9572-2.01010.22211520.20022594100
2.0101-2.06930.22721080.18082612100
2.0693-2.13610.22541420.17632609100
2.1361-2.21240.24951200.18532600100
2.2124-2.3010.21471610.18232578100
2.301-2.40570.21311460.18872632100
2.4057-2.53260.2671580.18722599100
2.5326-2.69120.24791290.17842645100
2.6912-2.8990.19751550.17242610100
2.899-3.19070.22371260.17732682100
3.1907-3.65240.18131470.15922658100
3.6524-4.60130.16331520.15712700100
4.6013-56.1750.20051460.17232860100
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)
14.554-0.63970.12820.5890.42354.2406-0.0638-0.20560.57170.3089-0.1036-0.574-0.34080.65560.24410.3507-0.0855-0.06680.3271-0.04910.288244.978512.684513.1585
24.0151.21771.67823.97561.60083.5256-0.0763-0.20210.11930.2178-0.15610.2334-0.0347-0.19770.18530.2977-0.03230.04730.1928-0.03760.170935.4839-4.15825.9289
33.4342.32641.06742.51391.01532.83980.5575-0.3262-1.06771.01140.2058-1.69030.85981.3937-0.28380.54630.0909-0.15980.7797-0.13770.757642.5967-19.819-6.4929
44.27191.1031.15134.54181.10494.1942-0.0197-0.37080.03410.0739-0.06830.3978-0.03310.16090.1380.2583-0.0299-0.00090.2631-0.04180.199230.1727-9.3211-3.5798
55.7853-0.4507-0.12154.10341.48625.4087-0.05930.3045-0.1823-0.08520.1701-0.71270.4440.43140.11010.30680.01810.07920.245-0.02110.173545.1527-4.17782.0467
62.8405-1.2766-2.23542.7751.05763.865-0.0391-0.0003-0.0559-0.07580.0227-0.0621-0.03670.11420.02510.2785-0.00930.01530.2103-0.00640.172134.969516.049513.5174
76.88330.56191.41744.82350.21863.6189-0.0310.10610.1309-0.2618-0.05380.2431-0.3085-0.640.23780.24390.0922-0.00090.3513-0.01920.168446.208-30.73617.8816
83.8160.50681.04043.15690.8012.6612-0.0337-0.28270.15010.06170.06230.156-0.2775-0.30870.08580.25580.03030.03130.2556-0.01940.148159.3826-31.807927.3178
95.02170.73480.38724.29480.24813.33330.08610.46160.2375-0.8553-0.1754-0.0317-0.5593-0.28330.19010.42110.057-0.00040.38090.01080.196856.5419-31.750214.8373
105.16640.31171.14682.10830.15493.5318-0.079-0.3450.16780.08870.0027-0.1733-0.29370.16120.03030.3043-0.01520.0220.307-0.0010.147865.741-31.246730.6239
115.35662.3888-0.46061.58170.03944.449-0.3211-0.1382-1.97641.52330.42020.13441.95510.156-0.13540.91590.0574-0.03460.73940.15140.67665.9815-45.367240.5401
126.4139-0.75742.00965.17510.74254.1707-0.1537-0.14580.6845-0.0601-0.2788-0.1402-0.82350.22990.0930.4128-0.0346-0.01510.3297-0.04970.258467.764-24.970831.345
132.36240.74221.88342.28110.52822.4680.3101-0.8587-0.06581.0068-0.21640.17070.3878-0.27910.05420.4611-0.04240.00970.5149-0.0220.162964.486-32.936539.085
143.1286-0.47431.22464.3625-1.38614.6277-0.1597-0.3461-0.47310.38050.09370.14990.1258-0.05580.09920.29390.00210.04490.30440.02290.186953.5058-37.189526.2368
152.4032-0.27920.34424.6524-1.84664.72840.3084-0.04760.0019-0.2478-0.10570.0746-0.3831-0.44930.07860.28120.07670.00970.2323-0.00920.148444.9148-20.708413.9797
162.712-0.57230.64775.5377-1.70374.6635-0.0778-0.26950.1280.5669-0.1-0.5298-0.43610.09840.02580.35560.04790.01970.37270.00880.23544.4039-26.84525.7182
172.31230.53880.28796.7986-1.11184.5441-0.0017-0.4825-0.30850.4061-0.1316-0.3047-0.08540.35710.05680.30450.05010.04190.3538-0.01680.182544.2553-27.713429.2158
183.8246-0.56621.11115.1371-1.84565.07320.3009-0.2482-0.1067-0.2686-0.1661-0.3202-0.3528-0.22250.12450.37620.04120.02390.31010.01350.17646.3866-15.147215.9348
194.45990.22730.87244.783-1.73484.30310.41280.5685-0.192-0.55730.23590.3970.6786-1.0371-0.14240.8536-0.0449-0.03931.00660.1570.689331.6492-19.68884.8244
202.3779-0.1975-0.97885.357-2.41472.8949-0.04640.06340.2162-0.5220.11570.4098-0.1939-0.25970.1240.53420.05960.04960.28070.04750.258443.5038-14.611811.0976
214.83720.75220.63241.7014-1.43426.2051-0.0225-0.41250.57470.8104-0.0204-0.4306-0.38540.13830.43770.56840.0691-0.05640.2865-0.07930.279546.3361-8.906717.1218
220.72640.5706-0.16380.62730.48342.13540.09870.1576-0.1478-0.8265-0.11070.21630.614-0.45830.01820.7132-0.0024-0.08980.3172-0.01350.214743.3473-18.94665.0607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 27 )A18 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 67 )A28 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 81 )A68 - 81
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 104 )A82 - 104
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 27 )B18 - 27
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 104 )B28 - 104
7X-RAY DIFFRACTION7chain 'D' and (resid 20 through 28 )D20 - 28
8X-RAY DIFFRACTION8chain 'D' and (resid 29 through 48 )D29 - 48
9X-RAY DIFFRACTION9chain 'D' and (resid 49 through 56 )D49 - 56
10X-RAY DIFFRACTION10chain 'D' and (resid 57 through 71 )D57 - 71
11X-RAY DIFFRACTION11chain 'D' and (resid 72 through 83 )D72 - 83
12X-RAY DIFFRACTION12chain 'D' and (resid 84 through 95 )D84 - 95
13X-RAY DIFFRACTION13chain 'D' and (resid 96 through 104 )D96 - 104
14X-RAY DIFFRACTION14chain 'C' and (resid 18 through 28 )C18 - 28
15X-RAY DIFFRACTION15chain 'C' and (resid 29 through 42 )C29 - 42
16X-RAY DIFFRACTION16chain 'C' and (resid 43 through 48 )C43 - 48
17X-RAY DIFFRACTION17chain 'C' and (resid 49 through 56 )C49 - 56
18X-RAY DIFFRACTION18chain 'C' and (resid 57 through 67 )C57 - 67
19X-RAY DIFFRACTION19chain 'C' and (resid 68 through 81 )C68 - 81
20X-RAY DIFFRACTION20chain 'C' and (resid 82 through 90 )C82 - 90
21X-RAY DIFFRACTION21chain 'C' and (resid 91 through 98 )C91 - 98
22X-RAY DIFFRACTION22chain 'C' and (resid 99 through 104 )C99 - 104

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