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- PDB-2ncd: NCD (NON-CLARET DISJUNCTIONAL) DIMER FROM D. MELANOGASTER -

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Basic information

Entry
Database: PDB / ID: 2ncd
TitleNCD (NON-CLARET DISJUNCTIONAL) DIMER FROM D. MELANOGASTER
ComponentsPROTEIN (Kinesin motor NCD)
KeywordsCONTRACTILE PROTEIN / KINESIN / MICROTUBULE-BASED MOTOR / NCD
Function / homology
Function and homology information


minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / microtubule bundle formation / spindle assembly involved in female meiosis / regulation of mitotic spindle assembly ...minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / microtubule bundle formation / spindle assembly involved in female meiosis / regulation of mitotic spindle assembly / mitotic centrosome separation / meiotic spindle / minus-end-directed microtubule motor activity / spindle organization / mitotic spindle assembly / mRNA transport / mitotic spindle organization / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / spindle / microtubule binding / hydrolase activity / cell division / centrosome / protein homodimerization activity / ATP binding / nucleus / cytosol
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein claret segregational
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSablin, E.P. / Case, R.B. / Dai, S.C. / Hart, C.L. / Ruby, A. / Vale, R.D. / Fletterick, R.J.
CitationJournal: Nature / Year: 1998
Title: Direction determination in the minus-end-directed kinesin motor ncd.
Authors: Sablin, E.P. / Case, R.B. / Dai, S.C. / Hart, C.L. / Ruby, A. / Vale, R.D. / Fletterick, R.J.
History
DepositionJun 4, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (Kinesin motor NCD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5476
Polymers47,7361
Non-polymers8115
Water97354
1
A: PROTEIN (Kinesin motor NCD)
hetero molecules

A: PROTEIN (Kinesin motor NCD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,09512
Polymers95,4722
Non-polymers1,62310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)123.000, 123.000, 121.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122

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Components

#1: Protein PROTEIN (Kinesin motor NCD)


Mass: 47735.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 281-700
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Description: BACTERIAL EXPRESSION / Gene: NCD / Plasmid: PHB40P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSE / References: UniProt: P20480
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.8 Å3/Da / Density % sol: 65 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: THE MOTHER LIQUOR CONTAINED PROTEIN AT ABOUT 20 MG/ML, 2 MM ADP, 10 MM MGCL2, 100 MM NACL, 700 MM LI2SO4, 1 MM EGTA, AND 1 MM DTT IN 20 MM HEPES, PH 7.5. THE RESERVOIR WAS 1.4 M LI2SO4, 10 ...Details: THE MOTHER LIQUOR CONTAINED PROTEIN AT ABOUT 20 MG/ML, 2 MM ADP, 10 MM MGCL2, 100 MM NACL, 700 MM LI2SO4, 1 MM EGTA, AND 1 MM DTT IN 20 MM HEPES, PH 7.5. THE RESERVOIR WAS 1.4 M LI2SO4, 10 MM MGCL2, 1 MM EGTA, 1 MM DTT IN 20 MM HEPES, PH 7.5., VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
22 mMADP1drop
310 mM1dropMgCl2
4100 mM1dropNaCl
5700 mM1dropLi2SO4
61 mMEGTA1drop
71 mMdithiothreitol1drop
820 mMHEPES1drop
91.4 M1reservoirLiSO4
1010 mM1reservoirMgCl2
111 mMEGTA1reservoir
121 mMdithiothreitol1reservoir
1320 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Oct 15, 1997
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 18795 / Num. obs: 18795 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5 / Rsym value: 0.13 / % possible all: 92.6
Reflection
*PLUS
Num. measured all: 190358
Reflection shell
*PLUS
% possible obs: 92.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NCD MONOMER

Resolution: 2.5→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 939 5 %RANDOM
Rwork0.226 ---
obs0.226 18795 98.6 %-
all-18795 --
Displacement parametersBiso mean: 23.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 47 54 2952
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d12.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.04
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.381.5
X-RAY DIFFRACTIONx_mcangle_it2.042
X-RAY DIFFRACTIONx_scbond_it2.182
X-RAY DIFFRACTIONx_scangle_it2.72.5
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.295 114 5 %
Rwork0.243 2257 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION3TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg12.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.04

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