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- PDB-5eyl: TUBULIN-BINDING DARPIN -

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Basic information

Entry
Database: PDB / ID: 5eyl
TitleTUBULIN-BINDING DARPIN
ComponentsDESIGNED ANKYRIN REPEAT PROTEIN (DARPIN)
KeywordsPROTEIN BINDING / DARPIN / MICROTUBULE / TUBULIN
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / PHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsAhmad, S. / Kossow, M. / Gigant, B.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0002-01 France
CitationJournal: Sci Rep / Year: 2016
Title: Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin.
Authors: Ahmad, S. / Pecqueur, L. / Dreier, B. / Hamdane, D. / Aumont-Nicaise, M. / Pluckthun, A. / Knossow, M. / Gigant, B.
History
DepositionNov 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN)
B: DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5607
Polymers36,0972
Non-polymers4635
Water1,53185
1
A: DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2353
Polymers18,0481
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3254
Polymers18,0481
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.311, 105.311, 192.962
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

PO4

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Components

#1: Protein DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN)


Mass: 18048.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PDST067 (PQE30 DERIVATIVE) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1BLUE
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: sodium acetate, sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.41→52.7 Å / Num. all: 16220 / Num. obs: 16124 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 54.31 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 10.4
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.6 / % possible all: 90

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DUI

4dui


Resolution: 2.41→44.38 Å / Cor.coef. Fo:Fc: 0.9476 / Cor.coef. Fo:Fc free: 0.8456 / SU R Cruickshank DPI: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.226 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 798 4.96 %RANDOM
Rwork0.1737 ---
obs0.1758 16079 99.13 %-
Displacement parametersBiso mean: 58.36 Å2
Baniso -1Baniso -2Baniso -3
1--5.6465 Å20 Å20 Å2
2---5.6465 Å20 Å2
3---11.293 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 2.41→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 29 85 2132
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012071HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.212811HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d711SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes302HARMONIC5
X-RAY DIFFRACTIONt_it2071HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion17.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion277SEMIHARMONIC5
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_contact2433SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.58 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2138 146 5.26 %
Rwork0.1987 2629 -
all0.1995 2775 -
obs--99.13 %
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)
11.3432-0.1526-0.80720.57031.44795.7987-0.04-0.0574-0.12480.0219-0.0720.0343-0.0287-0.29660.1119-0.09580.0520.0987-0.17160.0113-0.20025.6244-34.6906-13.1801
21.49950.0673-0.34117.0867-1.10020.8111-0.08480.05740.0472-0.82370.0924-0.0333-0.0840.0963-0.00760.1191-0.04520.0516-0.18690.0299-0.28624.3139-12.9405-18.8399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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