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- PDB-4l3i: Structure of the microtubule associated protein PRC1 (Protein Reg... -

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Basic information

Entry
Database: PDB / ID: 4l3i
TitleStructure of the microtubule associated protein PRC1 (Protein Regulator of Cytokinesis 1)
ComponentsProtein regulator of cytokinesis 1
KeywordsSTRUCTURAL PROTEIN / Spectrin / Helical / Coiled-coil / Microtubule binding / microtubule crosslinking / Spindle midzone
Function / homology
Function and homology information


contractile ring / mitotic spindle midzone assembly / mitotic spindle elongation / mitotic spindle midzone / RHO GTPases activate CIT / intercellular bridge / kinesin binding / regulation of cytokinesis / spindle microtubule / spindle pole ...contractile ring / mitotic spindle midzone assembly / mitotic spindle elongation / mitotic spindle midzone / RHO GTPases activate CIT / intercellular bridge / kinesin binding / regulation of cytokinesis / spindle microtubule / spindle pole / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / chromosome / midbody / microtubule binding / cell division / positive regulation of cell population proliferation / protein kinase binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Microtubule-associated protein, MAP65/Ase1/PRC1 / Microtubule associated protein (MAP65/ASE1 family)
Similarity search - Domain/homology
Protein regulator of cytokinesis 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6005 Å
AuthorsSubramanian, R. / Ti, S. / Tan, L. / Darst, S.A. / Kapoor, T.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Marking and Measuring Single Microtubules by PRC1 and Kinesin-4.
Authors: Subramanian, R. / Ti, S.C. / Tan, L. / Darst, S.A. / Kapoor, T.M.
History
DepositionJun 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein regulator of cytokinesis 1
B: Protein regulator of cytokinesis 1


Theoretical massNumber of molelcules
Total (without water)117,7722
Polymers117,7722
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-43 kcal/mol
Surface area54260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.205, 210.782, 112.294
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein regulator of cytokinesis 1


Mass: 58886.082 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-rosetta / References: UniProt: O43663

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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: 5.92 Å3/Da / Density % sol: 79.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Concentration: 5-10 mg/ml Protein buffer: 80 mM PIPES (pH 6.8), 1 mM MgCl2, 1 mM EGTA, 150 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.493
ReflectionResolution: 3.55→30 Å / Num. obs: 31794 / % possible obs: 96.2 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4
Reflection shellResolution: 3.55→3.68 Å / % possible all: 83.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AutoSol(phenix)phasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.6005→29.734 Å / σ(F): 0 / Phase error: 37.22 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2999 1969 6.47 %
Rwork0.2573 --
obs0.2617 30429 96.21 %
all-30429 -
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.212 Å2 / ksol: 0.243 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-70.2734 Å2-0 Å21.7719 Å2
2---56.7843 Å20 Å2
3----13.4892 Å2
Refinement stepCycle: LAST / Resolution: 3.6005→29.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6446 0 0 0 6446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036589
X-RAY DIFFRACTIONf_angle_d0.7628969
X-RAY DIFFRACTIONf_dihedral_angle_d12.0052256
X-RAY DIFFRACTIONf_chiral_restr0.0541064
X-RAY DIFFRACTIONf_plane_restr0.0031177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6005-3.69040.41951250.39871849X-RAY DIFFRACTION84
3.6904-3.790.40951340.37591957X-RAY DIFFRACTION85
3.79-3.90120.4341350.35841987X-RAY DIFFRACTION89
3.9012-4.02690.33051330.31781993X-RAY DIFFRACTION88
4.0269-4.17040.35081430.30942076X-RAY DIFFRACTION91
4.1704-4.33690.37961390.28992060X-RAY DIFFRACTION91
4.3369-4.53370.29441390.25612076X-RAY DIFFRACTION93
4.5337-4.77180.31391440.26212046X-RAY DIFFRACTION91
4.7718-5.06940.23311430.2572104X-RAY DIFFRACTION92
5.0694-5.45850.31251380.2792055X-RAY DIFFRACTION92
5.4585-6.00380.44781440.3452073X-RAY DIFFRACTION91
6.0038-6.86320.44441380.33892066X-RAY DIFFRACTION91
6.8632-8.61190.23321380.21912080X-RAY DIFFRACTION92
8.6119-29.73490.20531430.15882059X-RAY DIFFRACTION90

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