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- PDB-3vvv: Skich domain of NDP52 -

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Basic information

Entry
Database: PDB / ID: 3vvv
TitleSkich domain of NDP52
ComponentsCalcium-binding and coiled-coil domain-containing protein 2
KeywordsPROTEIN TRANSPORT / autophagy adaptor protein
Function / homology
Function and homology information


xenophagy / positive regulation of autophagosome maturation / autophagosome membrane / viral process / response to type II interferon / autophagosome / PML body / cytoplasmic vesicle / cytoskeleton / intracellular membrane-bounded organelle ...xenophagy / positive regulation of autophagosome maturation / autophagosome membrane / viral process / response to type II interferon / autophagosome / PML body / cytoplasmic vesicle / cytoskeleton / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Immunoglobulin-like - #2840 / SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Calcium-binding and coiled-coil domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsAkutsu, M. / Muhlinen, N.V. / Randow, F. / Komander, D.
CitationJournal: Mol.Cell / Year: 2012
Title: LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy
Authors: Muhlinen, N.V. / Akutsu, M. / Ravenhill, B.J. / Foeglein, A. / Bloor, S. / Rutherford, T.J. / Freund, S.M. / Komander, D. / Randow, F.
History
DepositionJul 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-binding and coiled-coil domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)14,5981
Polymers14,5981
Non-polymers00
Water3,207178
1
A: Calcium-binding and coiled-coil domain-containing protein 2

A: Calcium-binding and coiled-coil domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)29,1972
Polymers29,1972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-x-1,y-1/2,-z-1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.610, 37.460, 90.400
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 Calcium-binding and coiled-coil domain-containing protein 2 / Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 ...Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 / Nuclear dot protein 52


Mass: 14598.341 Da / Num. of mol.: 1 / Fragment: UNP residues 21-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCOCO2, NDP52 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13137
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 24% PEG4000, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.35→26.18 Å / Num. all: 27862 / Num. obs: 27862 / % possible obs: 99.3 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 2.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.35-1.423.50.5592.84013199.9
4.27-26.183.40.02328.3937193.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHENIXdev_723refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→23.266 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.9032 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 15.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 1361 4.89 %RANDOM
Rwork0.1546 ---
obs0.1562 27807 99.02 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.867 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 58.39 Å2 / Biso mean: 17.4049 Å2 / Biso min: 6.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.417 Å2-0 Å20 Å2
2---0.291 Å2-0 Å2
3---2.708 Å2
Refinement stepCycle: LAST / Resolution: 1.35→23.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 0 178 1083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01977
X-RAY DIFFRACTIONf_angle_d1.2721334
X-RAY DIFFRACTIONf_chiral_restr0.106131
X-RAY DIFFRACTIONf_plane_restr0.008175
X-RAY DIFFRACTIONf_dihedral_angle_d13.147350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.39830.23281150.199226452760100
1.3983-1.45420.25791340.185926172751100
1.4542-1.52040.2221320.168626142746100
1.5204-1.60050.19521280.13826372765100
1.6005-1.70080.17411400.126626372777100
1.7008-1.83210.15831430.11626442787100
1.8321-2.01630.16391860.129326102796100
2.0163-2.30790.18821350.14462658279399
2.3079-2.90680.17931210.16122654277597
2.9068-23.26930.20121270.17092730285795

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