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- PDB-7dbo: DPBB domain of VCP-like ATPase from Thermoplasma acidophilum -

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Basic information

Entry
Database: PDB / ID: 7dbo
TitleDPBB domain of VCP-like ATPase from Thermoplasma acidophilum
ComponentsVCP-like ATPase
KeywordsCHAPERONE / Double psi beta barrel
Function / homology
Function and homology information


intracellular membrane-bounded organelle / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 ...Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsYagi, S. / Tagami, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328 Japan
Citation
Journal: J.Am.Chem.Soc. / Year: 2021
Title: Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.
Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S.
#1: Journal: Biorxiv / Year: 2021
Title: Seven amino acid types suffice to reconstruct the core fold of RNA polymerase
Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S.
History
DepositionOct 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_id_ISSN / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VCP-like ATPase
B: VCP-like ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,88411
Polymers21,0192
Non-polymers8659
Water1,29772
1
A: VCP-like ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0867
Polymers10,5101
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VCP-like ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7984
Polymers10,5101
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.800, 118.800, 68.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-235-

HOH

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Components

#1: Protein VCP-like ATPase


Mass: 10509.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (acidophilic)
Gene: vat, Ta0840 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O05209
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM citrate / phosphate pH5.0, 1.4M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Feb 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 14642 / % possible obs: 99.7 % / Redundancy: 22.1 % / CC1/2: 0.995 / Rsym value: 0.114 / Net I/σ(I): 7.69
Reflection shellResolution: 1.9→2.02 Å / Mean I/σ(I) obs: 1.21 / Num. unique obs: 2292 / CC1/2: 0.615 / Rsym value: 1.331

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→41.07 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.62 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2642 1432 10.12 %
Rwork0.2168 12716 -
obs0.2217 14148 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.5 Å2 / Biso mean: 38.0305 Å2 / Biso min: 12.58 Å2
Refinement stepCycle: final / Resolution: 1.9→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 45 72 1500
Biso mean--45.24 41.24 -
Num. residues----177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.970.41531190.37181129124887
1.97-2.050.38071510.29911213136494
2.05-2.140.36281420.28391212135494
2.14-2.250.34181420.25961264140696
2.25-2.390.30371410.24611261140297
2.39-2.580.33641470.23181302144999
2.58-2.840.28111450.23841307145299
2.84-3.250.27951440.217813191463100
3.25-4.090.2111490.18113291478100
4.09-41.070.21321520.184713801532100

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