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- PDB-4lgm: Crystal Structure of Sulfolobus solfataricus Vps4 -

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Basic information

Entry
Database: PDB / ID: 4lgm
TitleCrystal Structure of Sulfolobus solfataricus Vps4
ComponentsVps4 AAA ATPase
KeywordsHYDROLASE / ATP hydrolysis
Function / homology
Function and homology information


vacuole organization / endosomal transport / ATP hydrolysis activity / ATP binding
Similarity search - Function
MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule 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 ...MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AAA family ATPase, p60 katanin
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.711 Å
AuthorsHan, H. / Hill, C.P. / Whitby, F.G. / Monroe, N.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The Oligomeric State of the Active Vps4 AAA ATPase.
Authors: Monroe, N. / Han, H. / Gonciarz, M.D. / Eckert, D.M. / Karren, M.A. / Whitby, F.G. / Sundquist, W.I. / Hill, C.P.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Apr 22, 2015Group: Structure summary
Revision 1.4Feb 28, 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

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Assembly

Deposited unit
A: Vps4 AAA ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6052
Polymers33,5701
Non-polymers351
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.321, 101.321, 64.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsThe functional unit is proposed to be hexamer. But it is monomeric in crystal

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Components

#1: Protein Vps4 AAA ATPase


Mass: 33569.797 Da / Num. of mol.: 1 / Fragment: UNP residues 85-372 / Mutation: E206Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0909 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZJ7, vesicle-fusing ATPase
#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.: 9 / 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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 70 % MPD, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Av σ(I) over netI: 14.06 / Number: 113696 / Rmerge(I) obs: 0.073 / Χ2: 1.03 / D res high: 2.73 Å / D res low: 30 Å / Num. obs: 19379 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.87309710.0490.9775.7
4.665.8710010.0660.9825.9
4.084.6610010.0760.9835.9
3.74.0810010.0861.0265.9
3.443.710010.1040.9746
3.243.4410010.1361.0255.9
3.073.2410010.1911.0875.9
2.943.0799.910.2821.0795.9
2.832.9410010.491.0785.9
2.732.8399.910.6571.0845.5
ReflectionResolution: 2.711→30 Å / Num. all: 19379 / Num. obs: 19379 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 85.65 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 26.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.711-2.835.50.657199.9
2.83-2.945.90.491100
2.94-3.075.90.282199.9
3.07-3.245.90.1911100
3.24-3.445.90.1361100
3.44-3.760.1041100
3.7-4.085.90.0861100
4.08-4.665.90.0761100
4.66-5.875.90.0661100
5.87-305.70.049197

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.711→23.166 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 1.36 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 1973 9.85 %
Rwork0.2171 --
obs0.2208 19379 99.41 %
all-20033 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.8882 Å2
Baniso -1Baniso -2Baniso -3
1--3.7374 Å20 Å20 Å2
2---3.7374 Å2-0 Å2
3---15.0566 Å2
Refinement stepCycle: LAST / Resolution: 2.711→23.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 1 9 2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072058
X-RAY DIFFRACTIONf_angle_d1.0032773
X-RAY DIFFRACTIONf_dihedral_angle_d14.271791
X-RAY DIFFRACTIONf_chiral_restr0.071312
X-RAY DIFFRACTIONf_plane_restr0.006351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.711-2.77860.33181360.31091217X-RAY DIFFRACTION95
2.7786-2.85360.35021300.28681319X-RAY DIFFRACTION100
2.8536-2.93740.39941520.2981301X-RAY DIFFRACTION100
2.9374-3.0320.31551450.25881282X-RAY DIFFRACTION100
3.032-3.14010.33671400.25041275X-RAY DIFFRACTION100
3.1401-3.26550.26351240.24971354X-RAY DIFFRACTION100
3.2655-3.41370.32911500.24891276X-RAY DIFFRACTION100
3.4137-3.5930.26491200.24351319X-RAY DIFFRACTION100
3.593-3.81720.251500.21431289X-RAY DIFFRACTION100
3.8172-4.11050.29041400.20261296X-RAY DIFFRACTION100
4.1105-4.52130.21241460.19691291X-RAY DIFFRACTION100
4.5213-5.16920.17391560.19341289X-RAY DIFFRACTION100
5.1692-6.48890.29421440.23431292X-RAY DIFFRACTION100
6.4889-23.16640.24181400.1921260X-RAY DIFFRACTION97

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