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- PDB-5z6q: Crystal structure of AAA of Spastin -

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Basic information

Entry
Database: PDB / ID: 5z6q
TitleCrystal structure of AAA of Spastin
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 / microtubule bundle formation / anterograde axonal transport / mitotic spindle disassembly / protein hexamerization / exit from mitosis / axonal transport of mitochondrion / beta-tubulin binding / positive regulation of cytokinesis / mitotic cytokinesis / alpha-tubulin binding / endoplasmic reticulum to Golgi vesicle-mediated transport / axon cytoplasm / lipid droplet / axonogenesis / isomerase activity / protein homooligomerization / spindle pole / midbody / cytoplasmic vesicle / microtubule binding / nuclear membrane / microtubule / endosome / axon / centrosome / endoplasmic reticulum membrane / protein-containing complex binding / 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 ...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
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: FEBS Lett. / Year: 2018
Title: The AAA protein spastin possesses two levels of basal ATPase activity
Authors: Fan, X. / Lin, Z. / Fan, G. / Lu, J. / Hou, Y. / Habai, G. / Sun, L. / Yu, P. / Shen, Y. / Wen, M. / Wang, C.
History
DepositionJan 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: 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)42,7802
Polymers42,7451
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.520, 90.520, 89.153
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: 42744.828 Da / Num. of mol.: 1 / Fragment: UNP residues 229-616
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)
References: UniProt: Q9UBP0, EC: 3.6.4.3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3M (NH4)2SO4, 100mM NH4Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→38.8 Å / Num. obs: 8390 / % possible obs: 100 % / Redundancy: 10 % / Net I/σ(I): 22.8
Reflection shellResolution: 3→3.43 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38.75 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35
RfactorNum. reflection% reflection
Rfree0.2755 389 4.64 %
Rwork0.1942 --
obs0.1981 8390 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 1 0 1965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011989
X-RAY DIFFRACTIONf_angle_d1.3242704
X-RAY DIFFRACTIONf_dihedral_angle_d18.262705
X-RAY DIFFRACTIONf_chiral_restr0.07334
X-RAY DIFFRACTIONf_plane_restr0.005351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9997-3.43350.3691290.27722656X-RAY DIFFRACTION100
3.4335-4.3250.30421250.20472656X-RAY DIFFRACTION100
4.325-38.75310.23621350.1662689X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -30.3827 Å / Origin y: 18.8872 Å / Origin z: 1.5619 Å
111213212223313233
T0.388 Å20.0123 Å20.0303 Å2-0.5688 Å2-0.09 Å2--0.451 Å2
L0.9481 °20.4134 °2-0.0871 °2-2.2818 °2-0.0377 °2--0.982 °2
S-0.1519 Å °0.1559 Å °-0.0311 Å °-0.1411 Å °0.0724 Å °-0.2287 Å °0.0269 Å °-0.0568 Å °0.0763 Å °
Refinement TLS groupSelection details: all

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