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- PDB-5w3d: The structure of kinesin-14 wild-type Ncd-ADP dimer -

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Basic information

Entry
Database: PDB / ID: 5w3d
TitleThe structure of kinesin-14 wild-type Ncd-ADP dimer
ComponentsProtein claret segregational
KeywordsMOTOR PROTEIN / NCD / MICROTUBULE / MOTOR / KINESIN / CELL CYCLE
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 / spindle assembly involved in female meiosis / minus-end-directed microtubule motor activity / 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 / spindle assembly involved in female meiosis / minus-end-directed microtubule motor activity / regulation of mitotic spindle assembly / microtubule bundle formation / meiotic spindle / mitotic centrosome separation / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 Å
AuthorsPark, H.W. / Ma, Z. / Chacko, J. / Jiang, S.M. / Robinson, R.C. / Endow, S.A.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis of small molecule ATPase inhibition of a human mitotic kinesin motor protein.
Authors: Park, H.W. / Ma, Z. / Zhu, H. / Jiang, S. / Robinson, R.C. / Endow, S.A.
History
DepositionJun 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein claret segregational
B: Protein claret segregational
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4236
Polymers93,5202
Non-polymers9034
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-60 kcal/mol
Surface area33840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.271, 67.249, 94.421
Angle α, β, γ (deg.)90.000, 97.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein claret segregational / Non-claret disjunctional


Mass: 46759.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ncd, CA(ND), CG7831 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20480
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50 mM sodium phosphate, 7 mM dithiothreitol, 10 mM magnesium chloride, 700 mM sodium chloride, 13% PEG8000 (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.789→93.521 Å / Num. all: 25309 / Num. obs: 25309 / % possible obs: 99.1 % / Redundancy: 5.8 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.1 / Rsym value: 0.091 / Net I/av σ(I): 6.2 / Net I/σ(I): 11.5 / Num. measured all: 146928
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.79-2.945.80.5331.52016534920.240.5860.5332.794.7
2.94-3.126.10.372.12105334780.1630.4050.37499.9
3.12-3.3360.2413.11992933020.1060.2630.241699.9
3.33-3.660.1514.91837830690.0670.1660.1519.399.9
3.6-3.945.90.171665328300.0440.1090.113.399.9
3.94-4.415.70.088.61474525700.0360.0880.0817.299.9
4.41-5.095.60.0699.71267822750.0320.0760.06920.3100
5.09-6.245.50.0719.11072319360.0320.0780.07117.699.9
6.24-8.825.40.05910817615030.0260.0650.05920.999.9
8.82-46.7615.20.04513.544288540.020.050.04528.699

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALA3.3.20data scaling
Cootmodel building
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N6M

1n6m


Resolution: 2.79→46.8 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.956 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 1288 5.1 %RANDOM
Rwork0.2353 ---
obs0.2376 24019 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.19 Å2 / Biso mean: 80.678 Å2 / Biso min: 40.95 Å2
Baniso -1Baniso -2Baniso -3
1-4 Å20 Å24.56 Å2
2--0.83 Å20 Å2
3----5.26 Å2
Refinement stepCycle: final / Resolution: 2.79→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 56 0 5348
Biso mean--86.52 --
Num. residues----667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195434
X-RAY DIFFRACTIONr_bond_other_d00.025093
X-RAY DIFFRACTIONr_angle_refined_deg1.291.977344
X-RAY DIFFRACTIONr_angle_other_deg3.609311704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.43824.411263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92915965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3471538
X-RAY DIFFRACTIONr_chiral_restr0.0740.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026083
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021253
LS refinement shellResolution: 2.789→2.862 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 86 -
Rwork0.312 1577 -
all-1663 -
obs--89.17 %

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