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- PDB-3hqd: Human kinesin Eg5 motor domain in complex with AMPPNP and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 3hqd
TitleHuman kinesin Eg5 motor domain in complex with AMPPNP and Mg2+
ComponentsKinesin-like protein KIF11
KeywordsMOTOR PROTEIN / kinesin / motor domain / ATP hydrolysis / mitosis / spindle protein / ATP-binding / Cell cycle / Cell division / Coiled coil / Microtubule / Nucleotide-binding / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement ...spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / spindle / spindle pole / mitotic spindle / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsParke, C.L. / Wojcik, E.J. / Kim, S. / Worthylake, D.K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: ATP Hydrolysis in Eg5 Kinesin Involves a Catalytic Two-water Mechanism.
Authors: Parke, C.L. / Wojcik, E.J. / Kim, S. / Worthylake, D.K.
History
DepositionJun 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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 protein KIF11
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4937
Polymers82,3372
Non-polymers1,1565
Water5,062281
1
A: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7944
Polymers41,1691
Non-polymers6253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6993
Polymers41,1691
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.500, 71.435, 94.846
Angle α, β, γ (deg.)90.00, 98.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kinesin-like protein KIF11 / / Kinesin-related motor protein Eg5 / Kinesin-like spindle protein HKSP / Thyroid receptor- ...Kinesin-related motor protein Eg5 / Kinesin-like spindle protein HKSP / Thyroid receptor-interacting protein 5 / TRIP-5 / Kinesin-like protein 1


Mass: 41168.738 Da / Num. of mol.: 2
Fragment: motor domain of human kinesin Eg5 (residues 1-369)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EG5, KIF11, KNSL1, TRIP5 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P52732
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 40 mM KH2PO4, 20% glycerol w/v, 15% PEG 8k w/v, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→28.69 Å / Num. all: 41542 / Num. obs: 41542 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 2.85 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.1188 / Rsym value: 0.089 / Net I/σ(I): 9.35
Reflection shellResolution: 2.19→2.29 Å / Redundancy: 1.89 % / Rmerge(I) obs: 0.5481 / Mean I/σ(I) obs: 2.27 / Rsym value: 0.335 / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
PROTEUM2data collection
SAINTdata reduction
PROTEUM2data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1X88 molecule A
Resolution: 2.19→25 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 4140 10 %RANDOM
Rwork0.224 ---
obs0.224 41127 99.6 %-
all-41531 --
Solvent computationBsol: 38.559 Å2
Displacement parametersBiso mean: 28.859 Å2
Baniso -1Baniso -2Baniso -3
1--2.937 Å20 Å2-0.99 Å2
2---0.358 Å20 Å2
3---3.295 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.19→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5482 0 69 281 5832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.608
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID
2.19-2.290.34225010.2966X-RAY DIFFRACTION
2.29-2.410.32055070.2694X-RAY DIFFRACTION
2.41-2.560.28875170.2545X-RAY DIFFRACTION
2.56-2.760.28065240.2404X-RAY DIFFRACTION
2.76-3.030.27295140.2239X-RAY DIFFRACTION
3.03-3.470.27415450.2326X-RAY DIFFRACTION
3.47-4.370.2195360.1918X-RAY DIFFRACTION
4.37-24.780.2264960.1899X-RAY DIFFRACTION
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3anp.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5phosphate.param

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