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- PDB-4gkq: Structure of the neck and C-terminal motor homology domain of ViK... -

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Basic information

Entry
Database: PDB / ID: 4gkq
TitleStructure of the 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: 2.99 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 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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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)66,5222
Polymers66,5222
Non-polymers00
Water181
1
A: SPINDLE POLE BODY-ASSOCIATED PROTEIN VIK1


Theoretical massNumber of molelcules
Total (without water)33,2611
Polymers33,2611
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)33,2611
Polymers33,2611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)197.000, 197.000, 50.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein SPINDLE POLE BODY-ASSOCIATED PROTEIN VIK1


Mass: 33260.988 Da / Num. of mol.: 2 / Fragment: UNP residues 302-584
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: CAGL0H00638g / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL Codon Plus / References: UniProt: Q6FSG8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 12% PEG8000, 0.05M MgCl2, 0.15M NaCl, 5% Ethylene glycol, 1mM TCEP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2010
RadiationMonochromator: Double crystal cryo-cooled Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.99→20 Å / Num. all: 14671 / Num. obs: 14501 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 103.571 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.99-3.070.9282.1363361076100
3.07-3.150.6313.0362341057100
3.15-3.240.4174.4560121019100
3.24-3.340.315.7459431006100
3.34-3.450.2227.725732972100
3.45-3.570.15610.155623953100
3.57-3.710.12612.255386915100
3.71-3.860.10214.575009849100
3.86-4.030.09416.064842824100
4.03-4.230.08618.124780813100
4.23-4.460.07619.984340738100
4.46-4.730.07421.264298733100
4.73-5.050.07521.313988680100
5.05-5.460.07521.583696633100
5.46-5.980.07621.413320571100
5.98-6.690.07621.633021516100
6.69-7.720.07422.172679461100
7.72-9.460.07621.8206638698.7
9.46-13.370.07118.8293322775.9
13.370.07217.992747243.1

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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 / Resolution: 2.99→19.8 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2896 / WRfactor Rwork: 0.2354 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.806 / SU B: 39.247 / SU ML: 0.33 / SU R Cruickshank DPI: 0.3711 / SU Rfree: 0.4068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 1444 10 %RANDOM
Rwork0.2137 ---
all0.2182 14671 --
obs0.2182 14499 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 201.29 Å2 / Biso mean: 113.981 Å2 / Biso min: 66.06 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å2-1.11 Å20 Å2
2---2.21 Å20 Å2
3---3.32 Å2
Refinement stepCycle: LAST / Resolution: 2.99→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 0 1 3324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023380
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9624598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73723.496123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.17615459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9861510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212500
LS refinement shellResolution: 2.99→3.066 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 106 -
Rwork0.291 938 -
all-1044 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7525-0.41610.98566.1721-0.49817.0757-0.2067-0.0615-0.43890.1765-0.19330.80270.44-0.47190.40.15580.01860.07710.1343-0.10970.2445134.8377142.91470.1948
26.6689-1.6942-0.76459.94050.85892.6593-0.22670.29370.9873-0.34220.4248-1.15710.00680.0621-0.19810.135-0.0973-0.03540.26030.05410.284194.6169138.8473-9.782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A300 - 582
2X-RAY DIFFRACTION2B311 - 582

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