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- PDB-4gkr: Structure of the C-terminal motor domain of Kar3 from Candida glabrata -

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Basic information

Entry
Database: PDB / ID: 4gkr
TitleStructure of the C-terminal motor domain of Kar3 from Candida glabrata
ComponentsNeck and C-terminal motor domain of Kar3
KeywordsSTRUCTURAL PROTEIN / Kinesin-14 motor domain with neck / ATPase / mitotic kinesin / Vik1
Function / homology
Function and homology information


minus-end directed microtubule sliding / 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 / kinesin complex / cytoplasmic microtubule / regulation of mitotic spindle organization / meiotic cell cycle ...minus-end directed microtubule sliding / 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 / kinesin complex / 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 / 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 motor domain-containing protein
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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.classification / _software.name
Revision 1.4Sep 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: Neck and C-terminal motor domain of Kar3
B: Neck and C-terminal motor domain of Kar3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8298
Polymers83,8022
Non-polymers1,0276
Water93752
1
A: Neck and C-terminal motor domain of Kar3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4154
Polymers41,9011
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neck and C-terminal motor domain of Kar3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4154
Polymers41,9011
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.707, 84.066, 151.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 350 - 685 / Label seq-ID: 29 - 364

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Neck and C-terminal motor domain of Kar3


Mass: 41901.152 Da / Num. of mol.: 2 / Fragment: UNP residues 324-692
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: CAGL0D04994g / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL Codon Plus / References: UniProt: Q6FVW6
#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 / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M MIB buffer, 25% PEG1500, 1mM TCEP, 1mM ATP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2009
RadiationMonochromator: Horizontal focusing Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 21478 / Num. obs: 20662 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Rmerge(I) obs: 0.076 / Χ2: 1.305 / Net I/σ(I): 18.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.69-2.810.70.63919441.77191.2
2.8-2.91110.48719311.736191.9
2.91-3.04110.31519681.739193.9
3.04-3.211.10.21320171.608195.6
3.2-3.411.20.13820431.445196.6
3.4-3.6611.30.09120821.249197.2
3.66-4.0311.70.06820870.994198.2
4.03-4.6212.60.05121391.069199.3
4.62-5.8113.60.04522001.018199.9
5.81-50130.05222510.834197.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Adxvpackagedata processing
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3kar

3kar


Resolution: 2.69→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2664 / WRfactor Rwork: 0.2214 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8267 / SU B: 22.056 / SU ML: 0.232 / SU R Cruickshank DPI: 0.9753 / SU Rfree: 0.3414 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.975 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 1058 5.1 %RANDOM
Rwork0.2104 ---
all0.2128 21478 --
obs0.2128 20610 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.24 Å2 / Biso mean: 49.4792 Å2 / Biso min: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2---0.79 Å20 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.69→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 64 52 4486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024514
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9546158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42723.865163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14315633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4211517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213346
Refine LS restraints NCS

Ens-ID: 1 / Number: 329 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.09 / Type: LOCAL / Weight: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.69→2.757 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 66 -
Rwork0.325 1125 -
all-1191 -
obs--84.71 %
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)
13.4424-0.64120.32172.8770.86832.5144-0.0252-0.20640.0362-0.0737-0.057-0.069-0.0960.16890.08230.1208-0.0376-0.01430.05420.02910.04783.58413.802231.5756
26.03770.44720.86641.98980.44222.1093-0.06720.42470.2361-0.1477-0.03690.1268-0.1543-0.04180.1040.14470.0041-0.02550.04510.01840.080432.005-1.17891.9912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A350 - 685
2X-RAY DIFFRACTION2B349 - 690

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