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- PDB-7dg7: DPBB domain of VCP-like ATPase from Methanopyrus kandleri -

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Basic information

Entry
Database: PDB / ID: 7dg7
TitleDPBB domain of VCP-like ATPase from Methanopyrus kandleri
ComponentsATPase of the AAA+ class
KeywordsCHAPERONE / Double psi beta barrel
Function / homology
Function and homology information


intein-mediated protein splicing / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / : / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IMIDAZOLE / ATPase of the AAA+ class
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.604 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: ATPase of the AAA+ class
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,65511
Polymers9,9941
Non-polymers66110
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-54 kcal/mol
Surface area4980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.078, 29.787, 42.155
Angle α, β, γ (deg.)90.000, 106.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATPase of the AAA+ class / VCP-like ATPase


Mass: 9993.531 Da / Num. of mol.: 1 / Fragment: DPBB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) (archaea)
Gene: MK0486 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TY20
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM imidazole/HCl pH7.8, 2M NaCl, 200mM Zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 21, 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: 10094 / % possible obs: 98.7 % / Redundancy: 13.2 % / CC1/2: 0.99 / Net I/σ(I): 22.97
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
AutoSolphasing
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.604→40.436 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.36 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2273 993 10 %
Rwork0.2065 8940 -
obs0.2086 9933 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.6 Å2 / Biso mean: 20.4052 Å2 / Biso min: 3.87 Å2
Refinement stepCycle: final / Resolution: 1.604→40.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 0 18 68 744
Biso mean--26.11 28.04 -
Num. residues----86
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6041-1.68870.29261330.2343120692
1.6887-1.79450.29021370.2299121395
1.7945-1.9330.29081390.2174126597
1.933-2.12750.23871420.2078128898
2.1275-2.43540.19681450.2071295100
2.4354-3.06820.23671450.2131314100
3.0682-40.4360.19341520.1911359100

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