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- PDB-3fpr: Crystal Structure of Evasin-1 -

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Basic information

Entry
Database: PDB / ID: 3fpr
TitleCrystal Structure of Evasin-1
ComponentsEvasin-1
KeywordsIMMUNE SYSTEM / novel fold / Glycoprotein / Secreted
Function / homology
Function and homology information


negative regulation of chemokine activity / chemokine binding / C-C chemokine binding / extracellular region
Similarity search - Function
Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #100 / Evasins Class A / Evasins Class A / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesRhipicephalus sanguineus (brown dog tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.63 Å
AuthorsDias, J.M. / Shaw, J.P.
Citation
Journal: Plos One / Year: 2009
Title: Structural basis of chemokine sequestration by a tick chemokine binding protein: the crystal structure of the complex between Evasin-1 and CCL3
Authors: Dias, J.M. / Losberger, C. / Deruaz, M. / Power, C.A. / Proudfoot, A.E.I. / Shaw, J.P.
#1: Journal: J.Biol.Chem. / Year: 2007
Title: Molecular cloning and characterization of a highly selective chemokine-binding protein from the tick Rhipicephalus sanguineus.
Authors: Frauenschuh, A. / Power, C.A. / Deruaz, M. / Ferreira, B.R. / Silva, J.S. / Teixeira, M.M. / Dias, J.M. / Martin, T. / Wells, T.N.C. / Proudfoot, A.E.I.
#2: Journal: J.Exp.Med. / Year: 2008
Title: Ticks produce highly selective chemokine binding proteins with antiinflammatory activity
Authors: Deruaz, M. / Frauenschuh, A. / Alessandri, A.L. / Dias, J.M. / Coelho, F.M. / Russo, R.C. / Ferreira, B.R. / Graham, G.J. / Shaw, J.P. / Wells, T.N.C. / Teixeira, M.M. / Power, C.A. / Proudfoot, A.E.I.
History
DepositionJan 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Evasin-1
D: Evasin-1


Theoretical massNumber of molelcules
Total (without water)22,6132
Polymers22,6132
Non-polymers00
Water3,387188
1
A: Evasin-1


Theoretical massNumber of molelcules
Total (without water)11,3061
Polymers11,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Evasin-1


Theoretical massNumber of molelcules
Total (without water)11,3061
Polymers11,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.604, 46.165, 99.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Evasin-1


Mass: 11306.446 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus sanguineus (brown dog tick)
Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Tn5 / References: UniProt: P0C8E7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3% (w/v) PEG 4000, 200mM Ammonium Sulfate, 10% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 18, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→39.6 Å / Num. obs: 23281 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.065 / Net I/σ(I): 15.4
Reflection shellResolution: 1.6→1.8 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.341 / % possible all: 65.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.63→25.73 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 1.937 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26511 1127 5 %RANDOM
Rwork0.22557 ---
all0.22743 21318 --
obs0.22743 21318 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.206 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.63→25.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 0 188 1418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221263
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9711719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90623.96658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2641511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02989
X-RAY DIFFRACTIONr_nbd_refined0.2030.2554
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.216
X-RAY DIFFRACTIONr_mcbond_it1.1581.5826
X-RAY DIFFRACTIONr_mcangle_it2.01121300
X-RAY DIFFRACTIONr_scbond_it2.8873490
X-RAY DIFFRACTIONr_scangle_it4.5164.5419
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 75 -
Rwork0.266 1162 -
obs--72.55 %

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