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- PDB-4d81: Metallosphera sedula Vps4 crystal structure -

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Basic information

Entry
Database: PDB / ID: 4d81
TitleMetallosphera sedula Vps4 crystal structure
ComponentsAAA ATPASE, CENTRAL DOMAIN PROTEINAAA proteins
KeywordsHYDROLASE / VPS4
Function / homology
Function and homology information


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 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...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 / 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
ADENOSINE-5'-DIPHOSPHATE / AAA ATPase, central domain protein
Similarity search - Component
Biological speciesMETALLOSPHAERA SEDULA (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCaillat, C. / Macheboeuf, P. / Wu, Y. / McCarthy, A.A. / Boeri-Erba, E. / Effantin, G. / Gottlinger, H.G. / Weissenhorn, W. / Renesto, P.
CitationJournal: Nat.Commun. / Year: 2015
Title: Asymmetric Ring Structure of Vps4 Required for Escrt-III Disassembly.
Authors: Caillat, C. / Macheboeuf, P. / Wu, Y. / Mccarthy, A.A. / Boeri-Erba, E. / Effantin, G. / Gottlinger, H.G. / Weissenhorn, W. / Renesto, P.
History
DepositionDec 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AAA ATPASE, CENTRAL DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6602
Polymers32,2321
Non-polymers4271
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.269, 65.269, 112.521
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 AAA ATPASE, CENTRAL DOMAIN PROTEIN / AAA proteins / VPS4


Mass: 32232.318 Da / Num. of mol.: 1 / Fragment: AAA, UNP RESIDUES 88-369
Source method: isolated from a genetically manipulated source
Details: TRUNCATION OF THE RESIDUES 1-74 / Source: (gene. exp.) METALLOSPHAERA SEDULA (archaea) / Plasmid: PDEST-17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A4YHC5, vesicle-fusing ATPase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.15 Å3/Da / Density % sol: 42.78 % / Description: NONE
Crystal growpH: 8.8
Details: 40% (W/V) POLYETHYLENE GLYCOL 200 (PEG200) 100 MM TRIS-HCL BUFFER (PH 8.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97375
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97375 Å / Relative weight: 1
ReflectionResolution: 2.4→56.5 Å / Num. obs: 12935 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→56.52 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.263 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 0.614 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26283 565 5.3 %RANDOM
Rwork0.20665 ---
obs0.20971 10038 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→56.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 27 7 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192181
X-RAY DIFFRACTIONr_bond_other_d0.0020.022144
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9932950
X-RAY DIFFRACTIONr_angle_other_deg0.8334944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.62124.28698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62815405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4941515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212387
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8675.1681050
X-RAY DIFFRACTIONr_mcbond_other3.8575.1661049
X-RAY DIFFRACTIONr_mcangle_it5.637.7371309
X-RAY DIFFRACTIONr_mcangle_other5.637.7391310
X-RAY DIFFRACTIONr_scbond_it4.6465.7711131
X-RAY DIFFRACTIONr_scbond_other4.6445.7711132
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.28.4271642
X-RAY DIFFRACTIONr_long_range_B_refined9.43442.1152527
X-RAY DIFFRACTIONr_long_range_B_other9.43442.1142527
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 48 -
Rwork0.25 731 -
obs--99.49 %

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