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- PDB-8fds: Ankyrin domain of SKD3 isoform 2 -

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Basic information

Entry
Database: PDB / ID: 8fds
TitleAnkyrin domain of SKD3 isoform 2
ComponentsCaseinolytic peptidase B protein homolog
KeywordsCHAPERONE / HYDROLASE / Mitochondria / Ankyrin
Function / homology
Function and homology information


granulocyte differentiation / RIG-I signaling pathway / ATP-dependent protein disaggregase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / antiviral innate immune response / mitochondrial intermembrane space / cellular response to heat / ATP hydrolysis activity / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / ATPase, AAA-type, core ...ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / ATPase, AAA-type, core / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FORMIC ACID / Mitochondrial disaggregase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLee, S. / Tsai, F.T.F. / Chang, C.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142143 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK115454 United States
Robert A. Welch FoundationQ-1530-20190330 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR140038 United States
National Institutes of Health/Office of the DirectorOD030246 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of impaired disaggregase function in the oxidation-sensitive SKD3 mutant causing 3-methylglutaconic aciduria.
Authors: Lee, S. / Lee, S.B. / Sung, N. / Xu, W.W. / Chang, C. / Kim, H.E. / Catic, A. / Tsai, F.T.F.
History
DepositionDec 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.2May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caseinolytic peptidase B protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6004
Polymers20,4621
Non-polymers1383
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-0 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.440, 60.440, 180.313
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

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Components

#1: Protein Caseinolytic peptidase B protein homolog / Suppressor of potassium transport defect 3


Mass: 20461.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPB, HSP78, SKD3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H078, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4 M potassium formate, 0.1 M Bis-Tris propane, pH 9.0, 2% w/v PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→52.34 Å / Num. obs: 24410 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.024 / Rrim(I) all: 0.104 / Net I/σ(I): 9
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 19.1 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1202 / CC1/2: 0.876 / Rpim(I) all: 0.125 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collect2data collection
DIALS3.6.2data reduction
DIALS3.6.2data scaling
PHASER2.8.3phasing
PHENIX1.20.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8DEH

8deh


Resolution: 1.65→52.34 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 1198 4.92 %
Rwork0.1991 --
obs0.2002 24341 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→52.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 9 57 1469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071479
X-RAY DIFFRACTIONf_angle_d0.8631994
X-RAY DIFFRACTIONf_dihedral_angle_d4.441203
X-RAY DIFFRACTIONf_chiral_restr0.049215
X-RAY DIFFRACTIONf_plane_restr0.007269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.720.32181340.33552480X-RAY DIFFRACTION99
1.72-1.80.3541460.29692490X-RAY DIFFRACTION100
1.8-1.890.30171260.26672516X-RAY DIFFRACTION100
1.89-2.010.2281170.22872545X-RAY DIFFRACTION100
2.01-2.160.23431180.19222542X-RAY DIFFRACTION100
2.16-2.380.231210.19582563X-RAY DIFFRACTION100
2.38-2.730.21771420.20172562X-RAY DIFFRACTION100
2.73-3.440.21691450.19432620X-RAY DIFFRACTION100
3.44-52.340.18951490.17282825X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -6.3794 Å / Origin y: 16.9263 Å / Origin z: -0.1808 Å
111213212223313233
T0.209 Å20.0025 Å2-0.0279 Å2-0.1835 Å2-0.0343 Å2--0.2014 Å2
L1.4124 °2-0.7193 °20.2622 °2-0.5948 °2-0.1093 °2--0.9694 °2
S-0.1877 Å °-0.0022 Å °0.0534 Å °0.1178 Å °0.1134 Å °-0.0493 Å °-0.0345 Å °-0.0886 Å °-0.0028 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 131 through 308)

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