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- PDB-1ry6: Crystal Structure of Internal Kinesin Motor Domain -

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Basic information

Entry
Database: PDB / ID: 1ry6
TitleCrystal Structure of Internal Kinesin Motor Domain
ComponentsINTERNAL KINESIN
KeywordsTRANSPORT PROTEIN / KINESIN MOTOR DOMAIN / NUCLEOTIDE-FREE
Function / homology
Function and homology information


kinesin complex / microtubule motor activity / microtubule-based movement / cytoskeletal motor activity / microtubule binding / ATP binding
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
Kinesin-13, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShipley, K. / Hekmat-Nejad, M. / Turner, J. / Moores, C. / Anderson, R. / Milligan, R. / Sakowicz, R. / Fletterick, R.
CitationJournal: Embo J. / Year: 2004
Title: Structure of a kinesin microtubule depolymerization machine.
Authors: Shipley, K. / Hekmat-Nejad, M. / Turner, J. / Moores, C. / Anderson, R. / Milligan, R. / Sakowicz, R. / Fletterick, R.
History
DepositionDec 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 350THE NATIVE FORM OF INTERNAL KINESIN IS A DIMER, BUT THE ENGINEERED FRAGMENT USED FOR THE STRUCTURE ...THE NATIVE FORM OF INTERNAL KINESIN IS A DIMER, BUT THE ENGINEERED FRAGMENT USED FOR THE STRUCTURE LACKS THE DIMERIZATION DOMAIN AND IT IS NOT CLEAR WHAT SYMMETRY OPERATION SHOULD BE USED TO CREATE A DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERNAL KINESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8582
Polymers40,7621
Non-polymers961
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.588, 105.588, 84.771
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein INTERNAL KINESIN


Mass: 40761.844 Da / Num. of mol.: 1 / Fragment: ATPASE 'MOTOR' DOMAIN (residues 68-396)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFL2165W / Plasmid: PCRT7-CT TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q8I4Y0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 3.85 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: ammonium sulfate, sodium nitrate, sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1272 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 21, 2001
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 86218 / Num. obs: 77888 / % possible obs: 90.3 % / Observed criterion σ(I): 60.2 / Redundancy: 3.2 % / Rsym value: 0.048 / Net I/σ(I): 15.52
Reflection shellResolution: 1.62→1.69 Å / Mean I/σ(I) obs: 1.75 / Rsym value: 0.369 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: KAR3, PDB entry 1F9T

1f9t


Resolution: 1.6→24.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.25 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23128 3326 5 %RANDOM
Rwork0.20545 ---
all0.2067 62677 --
obs0.20676 62677 91.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.595 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 5 306 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222562
X-RAY DIFFRACTIONr_bond_other_d0.0020.022360
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9723450
X-RAY DIFFRACTIONr_angle_other_deg0.96535523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925317
X-RAY DIFFRACTIONr_chiral_restr0.1230.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022790
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02484
X-RAY DIFFRACTIONr_nbd_refined0.2290.2537
X-RAY DIFFRACTIONr_nbd_other0.2530.22770
X-RAY DIFFRACTIONr_nbtor_other0.090.21472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.2236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.213
X-RAY DIFFRACTIONr_mcbond_it1.4231.51584
X-RAY DIFFRACTIONr_mcangle_it2.54622576
X-RAY DIFFRACTIONr_scbond_it3.4793978
X-RAY DIFFRACTIONr_scangle_it5.6754.5874
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.472 230
Rwork0.447 3888
obs-3888

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