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- PDB-3klt: Crystal structure of a vimentin fragment -

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Basic information

Entry
Database: PDB / ID: 3klt
TitleCrystal structure of a vimentin fragment
ComponentsVimentin
KeywordsSTRUCTURAL PROTEIN / 2A / L2 / alpha-helix / coiled-coil / parallel helices / Coiled coil / Intermediate filament / vimentin
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / microtubule organizing center / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton ...keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / microtubule organizing center / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / intermediate filament / cell leading edge / Bergmann glial cell differentiation / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / regulation of mRNA stability / Late endosomal microautophagy / structural constituent of cytoskeleton / cellular response to type II interferon / nuclear matrix / Aggrephagy / Chaperone Mediated Autophagy / neuron projection development / double-stranded RNA binding / negative regulation of neuron projection development / peroxisome / scaffold protein binding / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / cytoskeleton / protein domain specific binding / axon / focal adhesion / positive regulation of gene expression / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single helix bin / Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein ...Single helix bin / Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / SAMARIUM (III) ION / Vimentin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsNicolet, S. / Strelkov, S.V.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Atomic structure of vimentin coil 2.
Authors: Nicolet, S. / Herrmann, H. / Aebi, U. / Strelkov, S.V.
History
DepositionNov 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vimentin
B: Vimentin
C: Vimentin
D: Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,28219
Polymers33,2044
Non-polymers2,07715
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-75 kcal/mol
Surface area18530 Å2
MethodPISA
2
A: Vimentin
B: Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5928
Polymers16,6022
Non-polymers9906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-15 kcal/mol
Surface area11800 Å2
MethodPISA
3
C: Vimentin
D: Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,69011
Polymers16,6022
Non-polymers1,0889
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-14 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.200, 30.100, 82.980
Angle α, β, γ (deg.)90.00, 102.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Vimentin


Mass: 8301.084 Da / Num. of mol.: 4 / Fragment: UNP residues 263-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VIM / Plasmid: pET-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: P08670

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Non-polymers , 8 types, 22 molecules

#2: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Chemical ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sm
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 27% PEG monoethylether 550, 27mM CaCl2, 7.5% (v/v) glycerol, 10mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0720, 1.8449, 1.8457
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2008
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0721
21.84491
31.84571
ReflectionResolution: 2.6→44.44 Å / Num. obs: 15461 / % possible obs: 95.5 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 2.8 / Redundancy: 4.1 % / Biso Wilson estimate: 77.5 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 15.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→40.473 Å / SU ML: 0.94 / σ(F): 1.38 / Phase error: 36.77 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3311 909 5.88 %RANDOM
Rwork0.291 ---
obs0.2935 9176 94.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.795 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1915 Å20 Å21.8148 Å2
2---1.7878 Å20 Å2
3----4.9333 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 102 7 2399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022404
X-RAY DIFFRACTIONf_angle_d0.3693199
X-RAY DIFFRACTIONf_dihedral_angle_d14.511954
X-RAY DIFFRACTIONf_chiral_restr0.026339
X-RAY DIFFRACTIONf_plane_restr0.001421
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7001-2.86920.39541450.3513224589
2.8692-3.09070.3741790.3293240394
3.0907-3.40150.38711110.3063248695
3.4015-3.89340.29951240.2623248496
3.8934-4.90390.29711730.2483248797
4.9039-40.47790.32021770.2971244797

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