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- PDB-4frz: Arabidopsis KCBP motor domain dimerized via regulatory domain -

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Basic information

Entry
Database: PDB / ID: 4frz
TitleArabidopsis KCBP motor domain dimerized via regulatory domain
ComponentsKinesin-like calmodulin-binding protein
KeywordsMOTOR PROTEIN / kinesin motor domain / calmodulin binding motif / KCBP interacting calcium binding protein (KIC) / kinesin dimer
Function / homology
Function and homology information


trichome patterning / trichome branching / cortical microtubule / phragmoplast / cortical microtubule organization / minus-end-directed microtubule motor activity / microtubule bundle formation / microtubule motor activity / kinesin complex / microtubule-based movement ...trichome patterning / trichome branching / cortical microtubule / phragmoplast / cortical microtubule organization / minus-end-directed microtubule motor activity / microtubule bundle formation / microtubule motor activity / kinesin complex / microtubule-based movement / mitotic spindle / ADP binding / actin filament binding / microtubule binding / microtubule / oxidoreductase activity / cytoskeleton / calmodulin binding / calcium ion binding / protein kinase binding / protein homodimerization activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Prismane-like superfamily / Kinesin motor domain / Kinesin / Kinesin-like protein / FERM central domain ...MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Prismane-like superfamily / Kinesin motor domain / Kinesin / Kinesin-like protein / FERM central domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IMIDAZOLE / Kinesin-like protein KIN-14E
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVinogradova, M.
CitationJournal: Plos One / Year: 2013
Title: Plant Kinesin-Like Calmodulin Binding Protein Employs Its Regulatory Domain for Dimerization.
Authors: Vinogradova, M.V. / Malanina, G.G. / Waitzman, J.S. / Rice, S.E. / Fletterick, R.J.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_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 / _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: Kinesin-like calmodulin-binding protein
B: Kinesin-like calmodulin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,44713
Polymers88,0822
Non-polymers1,36611
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-14 kcal/mol
Surface area35350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.713, 75.068, 120.598
Angle α, β, γ (deg.)90.00, 91.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Kinesin-like calmodulin-binding protein / Protein ZWICHEL


Mass: 44040.949 Da / Num. of mol.: 2 / Fragment: UNP residues 875-1260 / Mutation: C1131N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: KCBP, ZWI, At5g65930, K14B20.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FHN8

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Non-polymers , 5 types, 109 molecules

#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


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


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG 3000, 100 mM imidazole (pH 8.0), 200 mM Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2008
RadiationMonochromator: double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 29651 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.41 / % possible all: 81.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SDM

1sdm


Resolution: 2.4→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rwork0.2254 --
all0.2629 32066 -
obs0.2629 29494 -
Rfree-2948 random
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5645 0 88 98 5831

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