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- PDB-7dg9: DPBB domain of VCP-like ATPase from Aeropyrum pernix -

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Basic information

Entry
Database: PDB / ID: 7dg9
TitleDPBB domain of VCP-like ATPase from Aeropyrum pernix
ComponentsCell division control protein 48, AAA family
KeywordsCHAPERONE / Double psi beta barrel
Function / homology
Function and homology information


cell division / ATP hydrolysis activity / ATP binding / metal ion binding
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
Cell division control protein 48, AAA family
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.602 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
DepositionNov 11, 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 1.2May 29, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 48, AAA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4236
Polymers10,0961
Non-polymers3275
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-56 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.040, 31.066, 94.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell division control protein 48, AAA family / VCP-like ATPase


Mass: 10095.523 Da / Num. of mol.: 1 / Fragment: DPBB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (archaea)
Gene: APE_1367 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9YC86
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.89 Å3/Da / Density % sol: 34.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Sodium acetate pH4.5, 20% PEG 1000, 200mM Zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 19200 / % possible obs: 98.8 % / Redundancy: 7.21 % / CC1/2: 0.999 / Net I/σ(I): 33.41
Reflection shellResolution: 1.6→1.7 Å / Num. unique obs: 1569 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.602→47.078 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 1922 10.01 %
Rwork0.1691 17276 -
obs0.1728 19198 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.08 Å2 / Biso mean: 14.9658 Å2 / Biso min: 4.23 Å2
Refinement stepCycle: final / Resolution: 1.602→47.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms687 0 5 138 830
Biso mean--24.79 26.85 -
Num. residues----90
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.602-1.64170.2121400.18681256100
1.6417-1.68610.23371390.17481250100
1.6861-1.73570.16981410.171268100
1.7357-1.79170.19621330.17021194100
1.7917-1.85580.22621470.17351282100
1.8558-1.93010.211330.16881257100
1.9301-2.01790.23091380.16921237100
2.0179-2.12430.18741390.16171239100
2.1243-2.25740.21281420.15961256100
2.2574-2.43170.26471380.16621243100
2.4317-2.67640.20741420.1681241100
2.6764-3.06360.19691370.17541249100
3.0636-3.85950.17491380.1586122498
3.8595-47.0780.21431150.1799108086

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