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- PDB-2owm: Motor domain of Neurospora crassa kinesin-3 (NcKin3) -

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Basic information

Entry
Database: PDB / ID: 2owm
TitleMotor domain of Neurospora crassa kinesin-3 (NcKin3)
ComponentsRelated to KINESIN-LIKE PROTEIN KIF1C
KeywordsMOTOR PROTEIN / kinesin / kinesin-3 / motor domain / ADP / neck linker
Function / homology
Function and homology information


microtubule motor activity / microtubule-based movement / microtubule binding / microtubule / ATP binding / metal ion binding
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase ...Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / 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 speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsMarx, A. / Muller, J. / Mandelkow, E.-M. / Woehlke, G. / Mandelkow, E.
CitationJournal: Biochemistry / Year: 2008
Title: X-ray Structure and Microtubule Interaction of the Motor Domain of Neurospora crassa NcKin3, a Kinesin with Unusual Processivity
Authors: Marx, A. / Muller, J. / Mandelkow, E.-M. / Woehlke, G. / Bouchet-Marquis, C. / Hoenger, A. / Mandelkow, E.
History
DepositionFeb 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_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: Related to KINESIN-LIKE PROTEIN KIF1C
B: Related to KINESIN-LIKE PROTEIN KIF1C
C: Related to KINESIN-LIKE PROTEIN KIF1C
D: Related to KINESIN-LIKE PROTEIN KIF1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,26812
Polymers198,4624
Non-polymers1,8068
Water00
1
A: Related to KINESIN-LIKE PROTEIN KIF1C
C: Related to KINESIN-LIKE PROTEIN KIF1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1346
Polymers99,2312
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
MethodPISA
2
B: Related to KINESIN-LIKE PROTEIN KIF1C
D: Related to KINESIN-LIKE PROTEIN KIF1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1346
Polymers99,2312
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.945, 98.408, 111.764
Angle α, β, γ (deg.)90.000, 91.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D
331A
341B
351C
361D
371A
381B
391C
401D
12A
22C
32A
42C
52A
62C
72A
82C
92A
102C
112A
122C
132A
142C
152A
162C
172A
182C
13B
23D
33B
43D
53B
63D
73B
83D
93B
103D
113B
123D
133B
143D
153B
163D
173B
183D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALASNASNAA40 - 13240 - 132
211VALVALASNASNBB40 - 13240 - 132
311VALVALASNASNCC40 - 13240 - 132
411VALVALASNASNDD40 - 13240 - 132
521THRTHRMETMETAA138 - 155138 - 155
621THRTHRMETMETBB138 - 155138 - 155
721THRTHRMETMETCC138 - 155138 - 155
821THRTHRMETMETDD138 - 155138 - 155
931GLYGLYALAALAAA162 - 176162 - 176
1031GLYGLYALAALABB162 - 176162 - 176
1131GLYGLYALAALACC162 - 176162 - 176
1231GLYGLYALAALADD162 - 176162 - 176
1341ASNASNLYSLYSAA188 - 218188 - 218
1441ASNASNLYSLYSBB188 - 218188 - 218
1541ASNASNLYSLYSCC188 - 218188 - 218
1641ASNASNLYSLYSDD188 - 218188 - 218
1751VALVALVALVALAA229 - 237229 - 237
1851VALVALVALVALBB229 - 237229 - 237
1951VALVALVALVALCC229 - 237229 - 237
2051VALVALVALVALDD229 - 237229 - 237
2161SERSERLYSLYSAA268 - 277268 - 277
2261SERSERLYSLYSBB268 - 277268 - 277
2361SERSERLYSLYSCC268 - 277268 - 277
2461SERSERLYSLYSDD268 - 277268 - 277
2571SERSERGLUGLUAA293 - 304293 - 304
2671SERSERGLUGLUBB293 - 304293 - 304
2771SERSERGLUGLUCC293 - 304293 - 304
2871SERSERGLUGLUDD293 - 304293 - 304
2981SERSERGLYGLYAA320 - 381320 - 381
3081SERSERGLYGLYBB320 - 381320 - 381
3181SERSERGLYGLYCC320 - 381320 - 381
3281SERSERGLYGLYDD320 - 381320 - 381
3391ALAALAILEILEAA387 - 413387 - 413
3491ALAALAILEILEBB387 - 413387 - 413
3591ALAALAILEILECC387 - 413387 - 413
3691ALAALAILEILEDD387 - 413387 - 413
37101MGMGADPADPAE - F1001 - 1002
38101MGMGADPADPBG - H1001 - 1002
39101MGMGADPADPCI - J1001 - 1002
40101MGMGADPADPDK - L1001 - 1002
112LYSLYSASNASNAA34 - 3934 - 39
212LYSLYSASNASNCC34 - 3934 - 39
322PHEPHEHISHISAA133 - 137133 - 137
422PHEPHEHISHISCC133 - 137133 - 137
532GLYGLYPROPROAA156 - 161156 - 161
632GLYGLYPROPROCC156 - 161156 - 161
742SERSERTYRTYRAA177 - 187177 - 187
842SERSERTYRTYRCC177 - 187177 - 187
952GLUGLUTYRTYRAA221 - 228221 - 228
1052GLUGLUTYRTYRCC221 - 228221 - 228
1162ARGARGARGARGAA238 - 267238 - 267
1262ARGARGARGARGCC238 - 267238 - 267
1372GLNGLNSERSERAA278 - 292278 - 292
1472GLNGLNSERSERCC278 - 292278 - 292
1582GLYGLYTHRTHRAA382 - 386382 - 386
1682GLYGLYTHRTHRCC382 - 386382 - 386
1792ARGARGVALVALAA414 - 422414 - 422
1892ARGARGVALVALCC414 - 422414 - 422
113ALAALAASNASNBB38 - 3938 - 39
213ALAALAASNASNDD38 - 3938 - 39
323PHEPHEHISHISBB133 - 137133 - 137
423PHEPHEHISHISDD133 - 137133 - 137
533GLYGLYPROPROBB156 - 161156 - 161
633GLYGLYPROPRODD156 - 161156 - 161
743SERSERTYRTYRBB177 - 187177 - 187
843SERSERTYRTYRDD177 - 187177 - 187
953VALVALTYRTYRBB219 - 228219 - 228
1053VALVALTYRTYRDD219 - 228219 - 228
1163ARGARGARGARGBB238 - 267238 - 267
1263ARGARGARGARGDD238 - 267238 - 267
1373GLNGLNSERSERBB278 - 292278 - 292
1473GLNGLNSERSERDD278 - 292278 - 292
1583GLYGLYTHRTHRBB382 - 386382 - 386
1683GLYGLYTHRTHRDD382 - 386382 - 386
1793ARGARGASPASPBB414 - 423414 - 423
1893ARGARGASPASPDD414 - 423414 - 423

NCS ensembles :
ID
1
2
3
DetailsThe biomolecule is a homodimer. This entry describes the asymmetric unit which contains 4 copies of the motor domain fragment of a protomer.

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Components

#1: Protein
Related to KINESIN-LIKE PROTEIN KIF1C / E.C.3.6.4.4 / NcKin3-434 / Related to KINESIN-LIKE PROTEIN KIF1C


Mass: 49615.383 Da / Num. of mol.: 4 / Fragment: motor domain (residues 1-434) / Mutation: CONFLICTS K88->E, N112->D, R281->G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Strain: WT 74 A / Gene: 17E5.250 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9C2M3, EC: 3.6.4.4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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

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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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 1.5ul protein solution (50mM phosphate buffer pH 7.5, 150mM sodium chloride, 50uM ATP, 1mM magnesium chloride, EGTA, DTT) mixed with 0.5ul reservoir (0.1M Hepes pH 7.5, 0.2M sodium potassium ...Details: 1.5ul protein solution (50mM phosphate buffer pH 7.5, 150mM sodium chloride, 50uM ATP, 1mM magnesium chloride, EGTA, DTT) mixed with 0.5ul reservoir (0.1M Hepes pH 7.5, 0.2M sodium potassium tartrate, 24% PEG3350) and 0.2ul 0.1M magnesium chloride , VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 7, 2004
RadiationMonochromator: SI[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 3.25→111.8 Å / Num. obs: 26100 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 6
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.705 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.25 Å30.32 Å
Translation3.25 Å30.32 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRUNCATED MODEL DERIVED FROM ADP COMPLEX OF KIF1A (1I5S)

1i5s


Resolution: 3.25→111.8 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.899 / SU B: 58.033 / SU ML: 0.431 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.547 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1329 5.1 %RANDOM
Rwork0.21 ---
obs0.213 24755 100 %-
all-26084 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å25.06 Å2
2--0.85 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 3.25→111.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10226 0 112 0 10338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02210542
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.97214343
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3851288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61823.066473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.912151709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5411593
X-RAY DIFFRACTIONr_chiral_restr0.1180.21646
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027929
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.25456
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3380.27143
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2409
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0730.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4250.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3861.56623
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.669210561
X-RAY DIFFRACTIONr_scbond_it1.12234368
X-RAY DIFFRACTIONr_scangle_it1.8674.53782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1889tight positional0.060.05
12B1889tight positional0.070.05
13C1889tight positional0.060.05
14D1889tight positional0.060.05
21A672tight positional0.060.05
31B684tight positional0.060.05
11A1889tight thermal0.110.5
12B1889tight thermal0.10.5
13C1889tight thermal0.110.5
14D1889tight thermal0.090.5
21A672tight thermal0.10.5
31B684tight thermal0.140.5
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 96 -
Rwork0.271 1798 -
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)
13.5897-1.1238-0.55233.3808-0.20044.22730.20540.01740.14380.0995-0.09-0.2002-0.3387-0.1666-0.1154-0.3595-0.12290.0129-0.4354-0.0229-0.382928.52833.9552.619
25.0351-1.27170.07512.295-1.07714.51590.27510.0958-0.1755-0.0821-0.1019-0.15670.0329-0.0623-0.1732-0.3168-0.0994-0.0459-0.3128-0.1066-0.314260.93421.152-3.237
33.76660.5976-1.35173.82170.69595.32750.18280.4797-0.2049-0.0903-0.11460.3165-0.1248-0.8742-0.0682-0.44770.0347-0.0728-0.11210.0072-0.339127.68925.5218.579
44.60831.2231-2.68164.7441-1.20676.2267-0.16960.538-0.4833-0.02620.2534-0.14350.679-0.7982-0.0838-0.2502-0.1843-0.07230.0017-0.0595-0.362180.95320.547-32.828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 422
2X-RAY DIFFRACTION2B38 - 423
3X-RAY DIFFRACTION3C34 - 422
4X-RAY DIFFRACTION4D38 - 423

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