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- PDB-5z6r: SPASTIN AAA WITH ATP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5z6r
TitleSPASTIN AAA WITH ATP
ComponentsSpastin
KeywordsHYDROLASE / SPASTIN
Function / homology
Function and homology information


cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III ...cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / membrane fission / exit from mitosis / microtubule bundle formation / anterograde axonal transport / mitotic spindle disassembly / protein hexamerization / axonal transport of mitochondrion / beta-tubulin binding / positive regulation of cytokinesis / mitotic cytokinesis / alpha-tubulin binding / metabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / axon cytoplasm / isomerase activity / lipid droplet / axonogenesis / protein homooligomerization / spindle pole / midbody / cytoplasmic vesicle / microtubule binding / nuclear membrane / microtubule / endosome / axon / centrosome / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Spastin, chordate / Spastin / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...Spastin, chordate / Spastin / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Spastin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLin, Z. / Wang, C. / Shen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: The Aaa Family Protein Spastin Severs A Microtubule
Authors: Lin, Z. / Wang, C. / Shen, Y.
History
DepositionJan 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spastin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2512
Polymers42,7441
Non-polymers5071
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-2 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.257, 87.257, 88.961
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Spastin / / Spastic paraplegia 4 protein


Mass: 42743.844 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 229-616 / Mutation: E442Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPAST, ADPSP, FSP2, KIAA1083, SPG4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): 'BL21-GOLD(DE3)PLYSS AG' / References: UniProt: Q9UBP0, EC: 3.6.4.3
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 25MM TRIS-HCL, 1MM DTT, 1MM MGCL2, 1MM ATP, 2% PEG 3350, 20MM KSCN
PH range: 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7753 / % possible obs: 99.8 % / Redundancy: 11.1 % / Net I/σ(I): 26.39
Reflection shellResolution: 3→3.1 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→28.8 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6
RfactorNum. reflection% reflection
Rfree0.279 350 4.67 %
Rwork0.215 --
obs0.219 7493 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 31 0 2022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122051
X-RAY DIFFRACTIONf_angle_d1.6982793
X-RAY DIFFRACTIONf_dihedral_angle_d16.522728
X-RAY DIFFRACTIONf_chiral_restr0.07335
X-RAY DIFFRACTIONf_plane_restr0.022359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.004-3.43810.37821020.27832240X-RAY DIFFRACTION92
3.4381-4.32930.31411280.2322425X-RAY DIFFRACTION99
4.3293-28.7980.21491200.1742478X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -30.2767 Å / Origin y: -16.4209 Å / Origin z: 3.1013 Å
111213212223313233
T0.1824 Å2-0.0042 Å20.0505 Å2-0.2004 Å20.0343 Å2--0.2003 Å2
L0.781 °2-0.9176 °20.5779 °2-1.815 °2-0.5937 °2--0.8729 °2
S-0.0302 Å °-0.0273 Å °0.1549 Å °-0.0653 Å °-0.0747 Å °-0.1833 Å °0.0788 Å °0.0721 Å °0.0124 Å °
Refinement TLS groupSelection details: ALL

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