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- PDB-6i31: Crystal structure of the tick chemokine-binding protein Evasin-3 -

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Basic information

Entry
Database: PDB / ID: 6i31
TitleCrystal structure of the tick chemokine-binding protein Evasin-3
ComponentsEvasin-3
KeywordsPEPTIDE BINDING PROTEIN / chemokine-binding tick evasin saliva
Function / homologynegative regulation of protein homodimerization activity / negative regulation of chemokine activity / C-X-C chemokine binding / extracellular region / : / Evasin-3
Function and homology information
Biological speciesRhipicephalus sanguineus (brown dog tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.79 Å
AuthorsDias, J.M. / Shaw, J.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationPG/16/100/32632 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: A knottin scaffold directs the CXC-chemokine-binding specificity of tick evasins.
Authors: Lee, A.W. / Deruaz, M. / Lynch, C. / Davies, G. / Singh, K. / Alenazi, Y. / Eaton, J.R.O. / Kawamura, A. / Shaw, J. / Proudfoot, A.E.I. / Dias, J.M. / Bhattacharya, S.
History
DepositionNov 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Evasin-3
B: Evasin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1383
Polymers14,0262
Non-polymers1121
Water1,74797
1
A: Evasin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1252
Polymers7,0131
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Evasin-3


Theoretical massNumber of molelcules
Total (without water)7,0131
Polymers7,0131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.090, 55.090, 71.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Evasin-3


Mass: 7012.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus sanguineus (brown dog tick)
Production host: Escherichia coli (E. coli) / References: UniProt: P0C8E8
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 25%PEG3350 100mM Bis-tris buffer pH 6.5 20mM CdCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.977 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.79→47.62 Å / Num. obs: 11993 / % possible obs: 98.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 26.31 Å2 / Rsym value: 0.066 / Net I/σ(I): 15
Reflection shellResolution: 1.79→1.97 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.79→14.4 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.213 577 4.81 %RANDOM
Rwork0.191 ---
obs0.192 11993 99.4 %-
Displacement parametersBiso mean: 42.33 Å2
Baniso -1Baniso -2Baniso -3
1--4.82 Å20 Å20 Å2
2---4.82 Å20 Å2
3---9.64 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.79→14.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms729 0 1 97 827
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01739HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13991HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d259SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes135HARMONIC5
X-RAY DIFFRACTIONt_it739HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion18.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion90SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact904SEMIHARMONIC4
LS refinement shellResolution: 1.79→1.97 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2313 157 5.63 %
Rwork0.1935 2633 -
all0.1955 2790 -
obs--98.48 %
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)
10.9731-0.9774-1.70821.56991.42722.83090.1031-0.0028-0.0194-0.0479-0.07920.0092-0.24450.0488-0.0240.00730.00450.0010.0232-0.035-0.01679.868429.10963.6287
22.794-0.681.73895.62042.8098.3155-0.13970.0391-0.34550.38930.16620.38810.3192-0.4442-0.0265-0.0528-0.05760.06630.02550.029-0.0250.248819.52017.2302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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