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- PDB-3tv0: Structure of dynactin p27 subunit -

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Basic information

Entry
Database: PDB / ID: 3tv0
TitleStructure of dynactin p27 subunit
ComponentsDynactin subunit 6
KeywordsSTRUCTURAL PROTEIN / left-handed beta-helix / p25 / p62 / Arp11 / cytosol
Function / homology
Function and homology information


dynactin complex / COPI-independent Golgi-to-ER retrograde traffic / dynein complex binding / COPI-mediated anterograde transport / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mitotic spindle organization / kinetochore / centrosome / cytosol
Similarity search - Function
Dynactin subunit 6 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1492 Å
AuthorsDerewenda, Z.S. / Derewenda, U. / Kowalska, A.
CitationJournal: To be Published
Title: Dynactin targets Polo-like kinase 1 to kinetochores
Authors: Derewenda, Z.S. / Derewenda, U. / Kowalska, A. / Zheng, M.
History
DepositionSep 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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: Dynactin subunit 6
B: Dynactin subunit 6


Theoretical massNumber of molelcules
Total (without water)42,1752
Polymers42,1752
Non-polymers00
Water1,33374
1
A: Dynactin subunit 6

B: Dynactin subunit 6


Theoretical massNumber of molelcules
Total (without water)42,1752
Polymers42,1752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area2530 Å2
ΔGint-11 kcal/mol
Surface area12170 Å2
MethodPISA
2
A: Dynactin subunit 6

A: Dynactin subunit 6

B: Dynactin subunit 6

B: Dynactin subunit 6


Theoretical massNumber of molelcules
Total (without water)84,3494
Polymers84,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area6820 Å2
ΔGint-34 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.960, 57.140, 80.190
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dynactin subunit 6 / Dynactin subunit p27 / Protein WS-3


Mass: 21087.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCTN6, WS3 / Production host: Escherichia coli (E. coli) / References: UniProt: O00399
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 3.6
Details: 19% PEG 2000, 0.15 M Potassium phosphate, pH 3.6, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2010 / Details: Si(111)
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.149→43.5 Å / Num. all: 16307 / Num. obs: 16255 / % possible obs: 81.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 5
Reflection shellResolution: 2.149→2.19 Å / % possible all: 38.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1492→43.451 Å / SU ML: 0.33 / σ(F): 1.36 / Phase error: 30.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 817 5.03 %random
Rwork0.2141 ---
obs0.2163 16255 81.14 %-
all-16307 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.955 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1492→43.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 0 74 2201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082178
X-RAY DIFFRACTIONf_angle_d1.1442961
X-RAY DIFFRACTIONf_dihedral_angle_d12.973822
X-RAY DIFFRACTIONf_chiral_restr0.074357
X-RAY DIFFRACTIONf_plane_restr0.005389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1492-2.28380.2905770.21551457X-RAY DIFFRACTION46
2.2838-2.46010.25021050.22341991X-RAY DIFFRACTION63
2.4601-2.70770.311330.24062646X-RAY DIFFRACTION84
2.7077-3.09940.29071680.22243018X-RAY DIFFRACTION96
3.0994-3.90450.24931680.19853127X-RAY DIFFRACTION99
3.9045-43.45950.23751660.21433199X-RAY DIFFRACTION98

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