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- PDB-3b9p: Spastin -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3b9p
TitleSpastin
ComponentsCG5977-PA, isoform A
KeywordsHYDROLASE / AAA ATPase / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


positive regulation of axon extension involved in regeneration / hemocyte migration / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / microtubule-severing ATPase / positive regulation of synaptic assembly at neuromuscular junction / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole ...positive regulation of axon extension involved in regeneration / hemocyte migration / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / microtubule-severing ATPase / positive regulation of synaptic assembly at neuromuscular junction / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole / microtubule severing / regulation of terminal button organization / positive regulation of lipid metabolic process / mitotic spindle elongation / positive regulation of microtubule depolymerization / negative regulation of microtubule depolymerization / protein hexamerization / positive regulation of dendrite morphogenesis / mitotic sister chromatid segregation / alpha-tubulin binding / lipid droplet / adult locomotory behavior / isomerase activity / locomotory behavior / neuromuscular junction / terminal bouton / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / chromosome / nervous system development / microtubule binding / microtubule / cell division / centrosome / ATP hydrolysis activity / ATP binding / membrane / cytoplasm
Similarity search - Function
Spastin / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site ...Spastin / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRoll-Mecak, A. / Vale, R.D.
CitationJournal: Nature / Year: 2008
Title: Structural basis of microtubule severing by the hereditary spastic paraplegia protein spastin.
Authors: Roll-Mecak, A. / Vale, R.D.
History
DepositionNov 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: CG5977-PA, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8882
Polymers32,8521
Non-polymers351
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.901, 83.901, 95.014
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 CG5977-PA, isoform A / CG5977-PB / isoform B


Mass: 32852.461 Da / Num. of mol.: 1 / Fragment: residues 463-758
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: spas / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IMX5, UniProt: Q8I0P1*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG400, 0.2M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 10099 / Redundancy: 4.1 % / Biso Wilson estimate: 64.8 Å2 / Rsym value: 0.055 / Net I/σ(I): 25.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 918 / Rsym value: 0.413

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.88 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 659210.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1006 10.3 %RANDOM
Rwork0.245 ---
obs0.245 9741 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.5425 Å2 / ksol: 0.295648 e/Å3
Displacement parametersBiso mean: 67.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.89 Å210.14 Å20 Å2
2--5.89 Å20 Å2
3----11.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 1 15 1989
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.081.5
X-RAY DIFFRACTIONc_mcangle_it3.462
X-RAY DIFFRACTIONc_scbond_it3.142
X-RAY DIFFRACTIONc_scangle_it4.62.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.452 132 10.2 %
Rwork0.397 1163 -
obs--74.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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