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- PDB-6st4: Crystal structure of the tick chemokine-binding protein Evasin-4 ... -

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Basic information

Entry
Database: PDB / ID: 6st4
TitleCrystal structure of the tick chemokine-binding protein Evasin-4 (SG 1)
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 / Evasin-4
Function and homology information
Biological speciesRhipicephalus sanguineus (brown dog tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.29 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 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Evasin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6876
Polymers11,3161
Non-polymers3705
Water1,17165
1
A: Evasin-4
hetero molecules

A: Evasin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,37312
Polymers22,6332
Non-polymers74110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Unit cell
Length a, b, c (Å)67.999, 67.999, 41.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Evasin-4


Mass: 11316.322 Da / Num. of mol.: 1
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 40% ethylene glycol, 0.2 M (NH4)2SO4, 0.1 M Phosphate-citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9772 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: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.29→58.89 Å / Num. obs: 28221 / % possible obs: 99.99 % / Redundancy: 9.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.143 / Net I/σ(I): 8.6
Reflection shellResolution: 1.29→1.32 Å / Rmerge(I) obs: 0.1511 / Num. unique obs: 2050 / CC1/2: 0.552

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREPphasing
SHELXDEphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.29→58.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.838 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.043
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 1452 5.1 %RANDOM
Rwork0.1781 ---
obs0.179 26769 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.32 Å2 / Biso mean: 29.285 Å2 / Biso min: 13.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.24 Å20 Å2
2---0.47 Å2-0 Å2
3---1.54 Å2
Refinement stepCycle: final / Resolution: 1.29→58.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms661 0 24 65 750
Biso mean--43.13 40.39 -
Num. residues----87
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.013712
X-RAY DIFFRACTIONr_bond_other_d0.0160.017583
X-RAY DIFFRACTIONr_angle_refined_deg1.821.665978
X-RAY DIFFRACTIONr_angle_other_deg1.6431.5591368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.072588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37925.45533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.9321588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.656151
X-RAY DIFFRACTIONr_chiral_restr0.0920.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02802
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02133
X-RAY DIFFRACTIONr_rigid_bond_restr6.63131295
LS refinement shellResolution: 1.29→1.323 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 103 -
Rwork0.296 1944 -
all-2047 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: 0.6151 Å / Origin y: 49.3452 Å / Origin z: 1.1446 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °-0 Å °

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