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- PDB-2v6y: Structure of the MIT domain from a S. solfataricus Vps4-like ATPase -

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Basic information

Entry
Database: PDB / ID: 2v6y
TitleStructure of the MIT domain from a S. solfataricus Vps4-like ATPase
Components(AAA FAMILY ATPASE, P60 KATANIN) x 2
KeywordsHYDROLASE / MIT / VPS4 / ARCHAEA / AAA-ATPASE / ATP-BINDING / MICROTUBULE INTERACTING AND TRAFFICKING DOMAIN / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
: / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site ...: / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
S,R MESO-TARTARIC ACID / AAA family ATPase, p60 katanin
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsObita, T. / Saksena, S. / Ghazi-Tabatabai, S. / Gill, D.J. / Perisic, O. / Emr, S.D. / Williams, R.L.
CitationJournal: Nature / Year: 2007
Title: Structural Basis for Selective Recognition of Escrt-III by the Aaa ATPase Vps4
Authors: Obita, T. / Saksena, S. / Ghazi-Tabatabai, S. / Gill, D.J. / Perisic, O. / Emr, S.D. / Williams, R.L.
History
DepositionJul 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AAA FAMILY ATPASE, P60 KATANIN
B: AAA FAMILY ATPASE, P60 KATANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0144
Polymers18,7142
Non-polymers3002
Water1448
1
A: AAA FAMILY ATPASE, P60 KATANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5142
Polymers9,3641
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: AAA FAMILY ATPASE, P60 KATANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5002
Polymers9,3501
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.178, 69.267, 123.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 1000
2113B1 - 1000

NCS oper: (Code: given
Matrix: (-0.003859, 0.061003, 0.99813), (0.110319, 0.992071, -0.060206), (-0.993889, 0.10988, -0.010558)
Vector: -33.1965, -16.3967, 28.9841)

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Components

#1: Protein AAA FAMILY ATPASE, P60 KATANIN / VPS4-LIKE AAA-ATPASE


Mass: 9363.847 Da / Num. of mol.: 1 / Fragment: MIT DOMAIN, RESIDUES 1-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: POPTH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q97ZJ7, vesicle-fusing ATPase
#2: Protein AAA FAMILY ATPASE, P60 KATANIN / VPS4-LIKE AAA-ATPASE


Mass: 9349.820 Da / Num. of mol.: 1 / Fragment: MIT DOMAIN, RESIDUES 1-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: POPTH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q97ZJ7, vesicle-fusing ATPase
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSSO0909 MIT DOMAIN

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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: 3.1 Å3/Da / Density % sol: 60.8 % / Description: NONE
Crystal growpH: 8
Details: RESERVOIR: 0.6 M AMMONIUM TARTRATE AND 2% PEG4K PROTEIN SOLUTION: 9 MG/ML IN 20 MM TRIS PH 8, 100 MM NACL, 2MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184
DetectorType: ADSC CCD / Detector: CCD / Details: TORROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→61.5 Å / Num. obs: 27901 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 99

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
autoSHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.4→61.66 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.901 / SU B: 18.134 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.248
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 463 4.8 %RANDOM
Rwork0.252 ---
obs0.253 9131 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å20 Å2
2--2.19 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.4→61.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 20 8 1213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221216
X-RAY DIFFRACTIONr_bond_other_d0.0030.028
X-RAY DIFFRACTIONr_angle_refined_deg1.3332.0061631
X-RAY DIFFRACTIONr_angle_other_deg0.952316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8665144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00524.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.85615245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.959156
X-RAY DIFFRACTIONr_chiral_restr0.1130.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02862
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2527
X-RAY DIFFRACTIONr_nbd_other0.3450.27
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2849
X-RAY DIFFRACTIONr_nbtor_other0.0330.24
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6891.5756
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91521178
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6793532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6864.5453
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
284tight positional0.070.05
288loose positional0.545
284tight thermal0.090.5
288loose thermal1.4510
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.44 37
Rwork0.314 675
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4973-1.9063-0.88714.12851.58278.6311-0.2261-0.06210.0406-0.35790.2814-0.06880.6112-0.3766-0.0554-0.1187-0.21120.0087-0.12870.117-0.2397-15.4157-1.583316.219
210.2286-3.08571.15746.8763-2.634910.4378-0.3664-0.0837-0.4569-0.52670.0619-0.44720.62660.89590.3045-0.2547-0.04850.1652-0.1407-0.0418-0.082314.282914.565216.7074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 75
2X-RAY DIFFRACTION1A1076
3X-RAY DIFFRACTION2B2 - 75
4X-RAY DIFFRACTION2B1076

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