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

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Basic information

Entry
Database: PDB / ID: 6stc
TitleCrystal structure of the tick chemokine-binding protein Evasin-4 (SG 2)
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: 1.69 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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)11,8127
Polymers11,3161
Non-polymers4956
Water88349
1
A: Evasin-4
hetero molecules

A: Evasin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,62414
Polymers22,6332
Non-polymers99112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)71.066, 71.066, 43.059
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.77 Å3/Da / Density % sol: 55.66 % / Description: hexagonal prism
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 40% PEG 400, 0.1 M NaAc pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.69→43.06 Å / Num. obs: 14083 / % possible obs: 98.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.7
Reflection shellResolution: 1.69→1.72 Å / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 722 / CC1/2: 0.496

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ST4

6st4


Resolution: 1.69→30.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.99 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.082
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 665 4.7 %RANDOM
Rwork0.1758 ---
obs0.1769 13399 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.19 Å2 / Biso mean: 32.411 Å2 / Biso min: 22.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å2-0 Å2
2--0.56 Å20 Å2
3----1.8 Å2
Refinement stepCycle: final / Resolution: 1.69→30.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 33 49 760
Biso mean--63.36 44.11 -
Num. residues----89
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013738
X-RAY DIFFRACTIONr_bond_other_d0.0010.017601
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.6571009
X-RAY DIFFRACTIONr_angle_other_deg1.5021.5551413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.035590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.13325.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5821592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.712151
X-RAY DIFFRACTIONr_chiral_restr0.0840.298
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02135
LS refinement shellResolution: 1.69→1.734 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 46 -
Rwork0.329 998 -
all-1044 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -26.639 Å / Origin y: 25.688 Å / Origin z: 9.112 Å
111213212223313233
T0.0495 Å2-0.0085 Å2-0.0085 Å2-0.032 Å20.0008 Å2--0.0701 Å2
L2.1745 °20.3461 °21.2674 °2-0.1633 °20.1097 °2--1.2113 °2
S0.068 Å °-0.0205 Å °-0.0049 Å °-0.0347 Å °-0.0212 Å °0.0273 Å °-0.0268 Å °0.0712 Å °-0.0468 Å °

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