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- PDB-4gkp: Structure of the truncated neck and C-terminal motor homology dom... -

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Basic information

Entry
Database: PDB / ID: 4gkp
TitleStructure of the truncated neck and C-terminal motor homology domain of ViK1 from Candida glabrata
ComponentsSpindle pole body-associated protein VIK1
KeywordsSTRUCTURAL PROTEIN / kinesin motor domain-like fold / Microtubule binding protein / Kinesin associated protein / Kar3
Function / homology
Function and homology information


kinesin complex / microtubule-based process / microtubule binding
Similarity search - Function
Kinesin - #20 / Spindle pole body-associated protein Vik1/Cik1, microtubule binding domain / Microtubule binding / Kinesin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Candida glabrata strain CBS138 chromosome H complete sequence
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsDuan, D. / Allingham, J.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Neck Rotation and Neck Mimic Docking in the Noncatalytic Kar3-associated Protein Vik1.
Authors: Duan, D. / Jia, Z. / Joshi, M. / Brunton, J. / Chan, M. / Drew, D. / Davis, D. / Allingham, J.S.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spindle pole body-associated protein VIK1
B: Spindle pole body-associated protein VIK1


Theoretical massNumber of molelcules
Total (without water)63,8052
Polymers63,8052
Non-polymers00
Water1,44180
1
A: Spindle pole body-associated protein VIK1


Theoretical massNumber of molelcules
Total (without water)31,9021
Polymers31,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Spindle pole body-associated protein VIK1


Theoretical massNumber of molelcules
Total (without water)31,9021
Polymers31,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.742, 77.722, 107.737
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spindle pole body-associated protein VIK1


Mass: 31902.449 Da / Num. of mol.: 2 / Fragment: UNP residues 313-584
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: CAGL0D00638G, CAGL0H00638g / Plasmid: Modified pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL codon + / References: UniProt: Q6FSG8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 13% PEG-6000, 5% isopropanol, 75mM NaAcetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 5, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.42→20 Å / Num. all: 22019 / Num. obs: 21752 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 49.904 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 37.65
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.42-2.50.1938.17101401880192.7
2.5-30.118.71660728260199.8
3-40.03546.565402866501100
4-60.02568.22777435031100
6-100.02668.988981187199.2
10-200.02569.061731272174.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O0A

2o0a


Resolution: 2.42→19.83 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2543 / WRfactor Rwork: 0.2074 / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8162 / SU B: 7.793 / SU ML: 0.184 / SU R Cruickshank DPI: 0.4339 / SU Rfree: 0.2752 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.434 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 1088 5 %RANDOM
Rwork0.2095 ---
all0.212 22019 --
obs0.212 21751 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.62 Å2 / Biso mean: 43.2617 Å2 / Biso min: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---1.25 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.42→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 0 80 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023806
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9565168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25424.911169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05315591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.827157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212860
LS refinement shellResolution: 2.42→2.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 71 -
Rwork0.272 1297 -
all-1368 -
obs--91.63 %

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