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- PDB-9umm: Giraffe KIF5A motor domain crystallized in the presence of 10 mM ADP -

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Basic information

Entry
Database: PDB / ID: 9umm
TitleGiraffe KIF5A motor domain crystallized in the presence of 10 mM ADP
ComponentsGcKIF5A
KeywordsMOTOR PROTEIN / Giraffe Kinesin motor KIF
Function / homologyACETATE ION
Function and homology information
Biological speciesGiraffa camelopardalis (giraffe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsImasaki, T. / Sakai, N. / Nitta, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJFR214K Japan
CitationJournal: To Be Published
Title: Enhanced Axonal Transport in Large Vertebrates: KIF5A Adaptations in Giraffes and Pythons
Authors: Kambara, T. / Rao, L. / Yamagishi, Y. / Ikeda, K. / Taniguchi, D. / Imasaki, T. / Shigematsu, H. / Sakai, N. / Gennerich, A. / Nitta, R. / Okada, Y.
History
DepositionApr 22, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GcKIF5A
B: GcKIF5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,40113
Polymers74,6812
Non-polymers72011
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-35 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.330, 50.310, 78.930
Angle α, β, γ (deg.)99.590, 107.250, 94.730
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GcKIF5A


Mass: 37340.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giraffa camelopardalis (giraffe) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 170 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate 0.4-0.5 M di-ammonium tartrate 0.1 M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→47.39 Å / Num. obs: 51367 / % possible obs: 97.4 % / Redundancy: 3.54 % / Biso Wilson estimate: 27.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.69
Reflection shellResolution: 1.95→2.07 Å / Num. unique obs: 8186 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIXv2.8refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.39 Å / SU ML: 0.2631 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.1524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2597 2505 4.88 %
Rwork0.2274 48845 -
obs0.229 51350 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.84 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 44 159 4615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754519
X-RAY DIFFRACTIONf_angle_d0.88316073
X-RAY DIFFRACTIONf_chiral_restr0.0541686
X-RAY DIFFRACTIONf_plane_restr0.0078776
X-RAY DIFFRACTIONf_dihedral_angle_d16.57091684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.3051210.2752622X-RAY DIFFRACTION94.62
1.99-2.030.34431450.26852695X-RAY DIFFRACTION96.53
2.03-2.070.29521370.26452692X-RAY DIFFRACTION96.65
2.07-2.120.31021350.24562718X-RAY DIFFRACTION96.55
2.12-2.170.28831480.24192673X-RAY DIFFRACTION96.88
2.17-2.230.28021330.23932682X-RAY DIFFRACTION96.9
2.23-2.30.25921340.23012737X-RAY DIFFRACTION97.09
2.3-2.370.25331420.22392672X-RAY DIFFRACTION97.03
2.37-2.460.27071420.22832713X-RAY DIFFRACTION97.34
2.46-2.550.28251330.24292728X-RAY DIFFRACTION97.38
2.55-2.670.27631440.23142739X-RAY DIFFRACTION98.36
2.67-2.810.27191380.22842752X-RAY DIFFRACTION98.07
2.81-2.990.25961330.23442720X-RAY DIFFRACTION97.94
2.99-3.220.28931450.23042742X-RAY DIFFRACTION98.16
3.22-3.540.261470.21862723X-RAY DIFFRACTION98.39
3.54-4.050.22011380.20632727X-RAY DIFFRACTION98.45
4.05-5.110.21511460.19412749X-RAY DIFFRACTION98.5
5.11-47.390.27051440.25052761X-RAY DIFFRACTION99.18

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