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- PDB-3t0q: Motor Domain Structure of the Kar3-like kinesin from Ashbya gossypii -

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Basic information

Entry
Database: PDB / ID: 3t0q
TitleMotor Domain Structure of the Kar3-like kinesin from Ashbya gossypii
ComponentsAGR253Wp
KeywordsMOTOR PROTEIN / Kinesin / Alpha and beta proteins / P-loop containing nucleoside triphosphate hydrolases / Microtubule Motor protein / ATP Binding
Function / homology
Function and homology information


nuclear migration involved in conjugation with cellular fusion / karyogamy involved in conjugation with cellular fusion / minus-end-directed microtubule motor activity / spindle pole body / mitotic sister chromatid cohesion / cytoplasmic microtubule / regulation of mitotic spindle organization / meiotic cell cycle / 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
ADENOSINE-5'-DIPHOSPHATE / Kinesin-like protein
Similarity search - Component
Biological speciesAshbya gossypii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDuan, D. / Hnatchuk, D.J. / Brenner, J. / Davis, D. / Allingham, J.S.
CitationJournal: Proteins / Year: 2012
Title: Crystal structure of the Kar3-like kinesin motor domain from the filamentous fungus Ashbya gossypii.
Authors: Duan, D. / Hnatchuk, D.J. / Brenner, J. / Davis, D. / Allingham, J.S.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_ref_seq_dif.details / _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: AGR253Wp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4284
Polymers39,9141
Non-polymers5143
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.866, 84.623, 101.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AGR253Wp


Mass: 39914.215 Da / Num. of mol.: 1 / Fragment: AgKar3 kinesin motor domain, UNP residues 365-709
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (fungus) / Strain: ATCC 10895 / Gene: AGOS_AGR253W, AGR253W, AGR253Wp / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL CodonPlus / References: UniProt: Q74ZE6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.81 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 14% PEG 3350, 125 mM sodium malonate, 1 mM TCEP and 0.1 M Bis-Tris propane pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 7, 2009
RadiationMonochromator: RH COATED SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.35→45 Å / Num. obs: 16073 / % possible obs: 95.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.244 / % possible all: 97.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAR

3kar


Resolution: 2.35→39.64 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 807 5.07 %
Rwork0.21 --
obs0.212 15916 95.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.93 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 37.91 Å2
Baniso -1Baniso -2Baniso -3
1-10.6732 Å2-0 Å2-0 Å2
2---4.4121 Å2-0 Å2
3----6.2611 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 32 96 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082386
X-RAY DIFFRACTIONf_angle_d1.2833242
X-RAY DIFFRACTIONf_dihedral_angle_d16.277843
X-RAY DIFFRACTIONf_chiral_restr0.093374
X-RAY DIFFRACTIONf_plane_restr0.006413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.49720.33141420.26682508X-RAY DIFFRACTION97
2.4972-2.690.33121380.24832516X-RAY DIFFRACTION98
2.69-2.96060.30621530.23612512X-RAY DIFFRACTION97
2.9606-3.38880.2691350.21022525X-RAY DIFFRACTION96
3.3888-4.26880.21021250.18442499X-RAY DIFFRACTION94
4.2688-39.64490.20711140.19712549X-RAY DIFFRACTION91

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