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- PDB-3fpt: The Crystal Structure of the Complex between Evasin-1 and CCL3 -

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Basic information

Entry
Database: PDB / ID: 3fpt
TitleThe Crystal Structure of the Complex between Evasin-1 and CCL3
ComponentsEvasin-1
KeywordsIMMUNE SYSTEM / novel fold / glycosylated protein / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShaw, J.P. / Dias, J.M.
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 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Evasin-1
B: Evasin-1
C: Evasin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2479
Polymers33,9193
Non-polymers1,3276
Water50428
1
A: Evasin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7493
Polymers11,3061
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Evasin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5282
Polymers11,3061
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Evasin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9704
Polymers11,3061
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.704, 70.491, 103.819
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.: 3
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): Sf9 / References: UniProt: P0C8E7
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23% (w/v) PEG 4000, 300mM Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 8, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→58 Å / Num. all: 26472 / Num. obs: 26472 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.08 / Net I/σ(I): 0.152
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.4 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3fpr

3fpr


Resolution: 2.7→32.62 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.863 / SU B: 11.315 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30521 717 5 %RANDOM
Rwork0.22605 ---
obs0.23005 13520 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 84 28 2007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0450.0222039
X-RAY DIFFRACTIONr_angle_refined_deg4.0492.0122780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.7865246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82124.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.87715303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.2891515
X-RAY DIFFRACTIONr_chiral_restr0.2380.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021549
X-RAY DIFFRACTIONr_nbd_refined0.3110.2891
X-RAY DIFFRACTIONr_nbtor_refined0.3580.21394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.23
X-RAY DIFFRACTIONr_mcbond_it2.0341.51293
X-RAY DIFFRACTIONr_mcangle_it3.48521990
X-RAY DIFFRACTIONr_scbond_it5.0973880
X-RAY DIFFRACTIONr_scangle_it7.7064.5790
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 56 -
Rwork0.361 959 -
obs--98.07 %

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