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- PDB-4dui: DARPIN D1 binding to tubulin beta chain (not in complex) -

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Basic information

Entry
Database: PDB / ID: 4dui
TitleDARPIN D1 binding to tubulin beta chain (not in complex)
ComponentsDESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D1
KeywordsDE NOVO PROTEIN / DARPIN / BETA-TUBULIN / TUBULIN / Artificial ankyrin repeat proteins / TUBULIN BETA CHAIN
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesARTIFICIAL GENE (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsPecqueur, L. / Duellberg, C. / Dreier, B. / Wang, Q. / Jiang, C. / Pluckthun, A. / Surrey, T. / Gigant, B. / Knossow, M.
CitationJournal: To be Published
Title: An Anti-Tubulin Darpin Caps the Microtubule Plus-End
Authors: Pecqueur, L. / Duellberg, C. / Dreier, B. / Wang, Q. / Jiang, C. / Pluckthun, A. / Surrey, T. / Gigant, B. / Knossow, M.
History
DepositionFeb 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5575
Polymers18,0841
Non-polymers4734
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.400, 43.400, 143.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D1


Mass: 18084.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTIFICIAL GENE (others) / Plasmid: PDST067 (pQE30 DERIVATIVE) / Production host: Escherichia coli (E. coli) / Strain (production host): XLIblue
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.86 Å3/Da / Density % sol: 33.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.02M CACL2, 0.1 NA ACETATE, 30% MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2011
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.16→41.53 Å / Num. obs: 48400 / % possible obs: 99.5 % / Observed criterion σ(F): 1.35 / Redundancy: 5.08 % / Biso Wilson estimate: 14.97 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.17
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.16-1.23197.8
1.23-1.311100
1.31-1.42199.9
1.42-1.551100
1.55-1.741100
1.74-2199.9
2-2.45199.8
2.45-3.46199.5

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XEE

2xee


Resolution: 1.16→32.103 Å / SU ML: 0.12 / σ(F): 1.35 / Phase error: 11.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1493 4840 10 %
Rwork0.1228 --
obs0.1254 48392 99.72 %
all-48528 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.689 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3291 Å2-0 Å20 Å2
2---0.3291 Å2-0 Å2
3---0.6581 Å2
Refinement stepCycle: LAST / Resolution: 1.16→32.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 32 167 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131365
X-RAY DIFFRACTIONf_angle_d1.81875
X-RAY DIFFRACTIONf_dihedral_angle_d13.824494
X-RAY DIFFRACTIONf_chiral_restr0.083223
X-RAY DIFFRACTIONf_plane_restr0.007243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1601-1.17330.25571570.21241408X-RAY DIFFRACTION98
1.1733-1.18710.21671550.17361401X-RAY DIFFRACTION99
1.1871-1.20150.20061590.16351425X-RAY DIFFRACTION99
1.2015-1.21680.17441560.16191408X-RAY DIFFRACTION100
1.2168-1.23280.20531590.15081426X-RAY DIFFRACTION100
1.2328-1.24970.2051590.14571433X-RAY DIFFRACTION100
1.2497-1.26750.18721570.13831417X-RAY DIFFRACTION100
1.2675-1.28640.18941600.14071436X-RAY DIFFRACTION100
1.2864-1.30650.18531590.13391429X-RAY DIFFRACTION100
1.3065-1.3280.16731590.12081439X-RAY DIFFRACTION100
1.328-1.35090.15991590.1111427X-RAY DIFFRACTION100
1.3509-1.37540.14821580.11271417X-RAY DIFFRACTION100
1.3754-1.40190.14821610.11041457X-RAY DIFFRACTION100
1.4019-1.43050.15411590.09961434X-RAY DIFFRACTION100
1.4305-1.46160.1451610.09641443X-RAY DIFFRACTION100
1.4616-1.49560.14221620.09681464X-RAY DIFFRACTION100
1.4956-1.5330.13441580.09021418X-RAY DIFFRACTION100
1.533-1.57440.13561600.08841441X-RAY DIFFRACTION100
1.5744-1.62080.12081610.09951452X-RAY DIFFRACTION100
1.6208-1.67310.13431630.09751458X-RAY DIFFRACTION100
1.6731-1.73290.12721610.10231447X-RAY DIFFRACTION100
1.7329-1.80220.12711620.10151467X-RAY DIFFRACTION100
1.8022-1.88430.11451610.10131441X-RAY DIFFRACTION100
1.8843-1.98360.14081630.11021471X-RAY DIFFRACTION100
1.9836-2.10780.12071630.10391470X-RAY DIFFRACTION100
2.1078-2.27060.1281640.11031479X-RAY DIFFRACTION100
2.2706-2.4990.13151650.10821475X-RAY DIFFRACTION99
2.499-2.86040.13281670.11921501X-RAY DIFFRACTION100
2.8604-3.6030.15641710.12941544X-RAY DIFFRACTION100
3.603-32.11550.17751810.16491624X-RAY DIFFRACTION99

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