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- PDB-1cz7: THE CRYSTAL STRUCTURE OF A MINUS-END DIRECTED MICROTUBULE MOTOR P... -

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Basic information

Entry
Database: PDB / ID: 1cz7
TitleTHE CRYSTAL STRUCTURE OF A MINUS-END DIRECTED MICROTUBULE MOTOR PROTEIN NCD REVEALS VARIABLE DIMER CONFORMATIONS
ComponentsMICROTUBULE MOTOR PROTEIN NCD
KeywordsCONTRACTILE PROTEIN / NCD CRYSTAL STRUCTURE / MICROTUBULE MOTORS / KINESIN SUPERFAMILY
Function / homologyKinesin motor domain profile. / Kinesin motor domain signature. / Kinesin motor domain / Kinesin motor domain superfamily / Kinesin-like protein / P-loop containing nucleoside triphosphate hydrolase / Kinesin motor domain, conserved site / Kinesin motor domain / spindle assembly involved in female meiosis / minus-end directed microtubule sliding ...Kinesin motor domain profile. / Kinesin motor domain signature. / Kinesin motor domain / Kinesin motor domain superfamily / Kinesin-like protein / P-loop containing nucleoside triphosphate hydrolase / Kinesin motor domain, conserved site / Kinesin motor domain / spindle assembly involved in female meiosis / minus-end directed microtubule sliding / spindle assembly involved in meiosis / regulation of mitotic spindle elongation / distributive segregation / mitotic spindle microtubule / mitotic spindle elongation / meiotic spindle organization / ATP-dependent microtubule motor activity, minus-end-directed / microtubule bundle formation / regulation of mitotic spindle assembly / meiotic spindle / mitotic centrosome separation / kinesin complex / microtubule motor activity / mRNA transport / spindle organization / microtubule-based movement / mitotic spindle assembly / mitotic spindle organization / mitotic spindle / chromosome segregation / spindle / microtubule / microtubule binding / ATPase activity / centrosome / cell division / protein homodimerization activity / ATP binding / nucleus / cytosol / Protein claret segregational
Function and homology information
Specimen sourceDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.9 Å resolution
AuthorsKozielski, F.K. / De Bonis, S. / Burmeister, W. / Cohen-Addad, C. / Wade, R.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of the minus-end-directed microtubule motor protein ncd reveals variable dimer conformations.
Authors: Kozielski, F. / De Bonis, S. / Burmeister, W.P. / Cohen-Addad, C. / Wade, R.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 1, 1999 / Release: Nov 5, 1999
RevisionDateData content typeGroupProviderType
1.0Nov 5, 1999Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MICROTUBULE MOTOR PROTEIN NCD
B: MICROTUBULE MOTOR PROTEIN NCD
C: MICROTUBULE MOTOR PROTEIN NCD
D: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,27412
Polyers184,4684
Non-polymers1,8068
Water2,666148
1
A: MICROTUBULE MOTOR PROTEIN NCD
B: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1376
Polyers92,2342
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3320
ΔGint (kcal/M)-52
Surface area (Å2)32230
MethodPISA
2
C: MICROTUBULE MOTOR PROTEIN NCD
D: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1376
Polyers92,2342
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4650
ΔGint (kcal/M)-62
Surface area (Å2)35480
MethodPISA
3
C: MICROTUBULE MOTOR PROTEIN NCD
D: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules

C: MICROTUBULE MOTOR PROTEIN NCD
D: MICROTUBULE MOTOR PROTEIN NCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,27412
Polyers184,4684
Non-polymers1,8068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area (Å2)10740
ΔGint (kcal/M)-125
Surface area (Å2)69520
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)116.194, 148.827, 261.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC 2 2 21

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Components

#1: Protein/peptide
MICROTUBULE MOTOR PROTEIN NCD / NCD / CLARET SEGREGATIONAL PROTEIN


Mass: 46117.004 Da / Num. of mol.: 4 / Fragment: CONSTRUCT MC5 FROM NCD / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Genus: Drosophila / Plasmid name: PET / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P20480
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / Magnesium
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Formula: H2O / Water

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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: 3.06 / Density percent sol: 59.85 %
Crystal growTemp: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, NACL, MGCL2, K3PO4, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal
*PLUS
Density percent sol: 58.6 %
Crystal grow
*PLUS
Temp: 20 ℃ / pH: 6.8
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
15 mg/mlprotein1drop
26.8 %PEG80001drop
31 M1dropNaCl
42 mMATP1drop
53.5 mMdithiothreitol1drop
610 mM1dropMgCl2
725 mMsodium phosphate1drop
825 mMsodium phophate1reservoir
913.5 %PEG80001reservoir
102 M1reservoirNaCl
117 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID14-4 / Synchrotron site: ESRF / Beamline: ID14-4 / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: CCD / Collection date: Dec 20, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 / Relative weight: 1
ReflectionD resolution high: 2.9 / D resolution low: 4 / Number all: 50539 / Number obs: 48773 / Observed criterion sigma I: 1 / Rmerge I obs: 0.085 / Percent possible obs: 96.5
Reflection shellHighest resolution: 2.9
Reflection
*PLUS
Number measured all: 136320
Reflection shell
*PLUS
Lowest resolution: 3 / Rmerge I obs: 0.28

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineDetails: SIMULATED ANNEALING, NCS / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 2 / Stereochemistry target values: ENGH & HUBER
Displacement parametersAniso B11: 14.632 / Aniso B12: 0 / Aniso B13: 0 / Aniso B22: 15.315 / Aniso B23: 0 / Aniso B33: -29.946
Least-squares processR factor R free: 0.294 / R factor R work: 0.258 / R factor obs: 0.258 / Highest resolution: 2.9 / Lowest resolution: 4 / Number reflection R free: 2463 / Number reflection all: 50539 / Number reflection obs: 48773 / Percent reflection R free: 5 / Percent reflection obs: 96.5
Refine hist #LASTHighest resolution: 2.9 / Lowest resolution: 4
Number of atoms included #LASTProtein: 11179 / Nucleic acid: 0 / Ligand: 112 / Solvent: 148 / Total: 11439
Software
*PLUS
Name: CNS / Classification: refinement
Refine
*PLUS
Sigma F: 2
Least-squares process
*PLUS
Highest resolution: 2.9 / Lowest resolution: 4 / Percent reflection R free: 5
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6

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