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- PDB-1gk7: HUMAN VIMENTIN COIL 1A FRAGMENT (1A) -

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Basic information

Entry
Database: PDB / ID: 1gk7
TitleHUMAN VIMENTIN COIL 1A FRAGMENT (1A)
ComponentsVIMENTIN
KeywordsVIMENTIN / INTERMEDIATE FILAMENT / HEPTAD REPEAT
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 / cellular response to type II interferon / structural constituent of cytoskeleton / nuclear matrix / Aggrephagy / Chaperone Mediated Autophagy / double-stranded RNA binding / neuron projection development / 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
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
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsStrelkov, S.V. / Herrmann, H. / Geisler, N. / Zimbelmann, R. / Aebi, U. / Burkhard, P.
Citation
Journal: Embo J. / Year: 2002
Title: Conserved Segments 1A and 2B of the Intermediate Filament Dimer: Their Atomic Structures and Role in Filament Assembly.
Authors: Strelkov, S. / Herrmann, H. / Geisler, N. / Wedig, T. / Zimbelmann, R. / Aebi, U. / Burkhard, P.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Divide-and-Conquer Crystallographic Approach Towards an Atomic Structure of Intermediate Filaments
Authors: Strelkov, S.V. / Herrmann, H. / Geisler, N. / Lustig, A. / Ivaninskii, S. / Zimbelmann, R. / Burkhard, P. / Aebi, U.
History
DepositionAug 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VIMENTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7502
Polymers4,6541
Non-polymers961
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.770, 56.770, 58.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-2026-

HOH

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Components

#1: Protein/peptide VIMENTIN


Mass: 4654.214 Da / Num. of mol.: 1 / Fragment: 1A, RESIDUES 102-138
Source method: isolated from a genetically manipulated source
Details: TWO EXTRA RESIDUES, GS, AT THE N-TERMINUS ARE RESULT OF THE CLONING PROCEDURE
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08670
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING USED IN THE LITERATURE FOR VIMENTIN DIFFERS BY +1 FROM THE NUMBERING USED IN ...THE RESIDUE NUMBERING USED IN THE LITERATURE FOR VIMENTIN DIFFERS BY +1 FROM THE NUMBERING USED IN SWISSPROT ENTRY P08670 THE FRAGMENT CONTAINS RESIDUES 102 TO 138 AND TWO EXOGENOUS RESIDUES, GS, AT THE N-TERMINUS

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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: 2.9 Å3/Da / Density % sol: 59 % / Description: THE SEARCH MODEL WAS A SINGLE CHAIN
Crystal growpH: 6.5
Details: 2.0M AMMONIUM ACETATE, 10%(V/V) DIOXANE, 0.1M MES/NA, PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorDetector: IMAGE PLATE / Date: Apr 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 11440 / % possible obs: 99.7 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 17
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZTA

2zta


Resolution: 1.4→49.39 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.967 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 461 4 %RANDOM
Rwork0.197 ---
obs0.198 10979 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.4→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms328 0 5 35 368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021341
X-RAY DIFFRACTIONr_bond_other_d0.0010.02310
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.0341.996456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.8563725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.250
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02371
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0264
X-RAY DIFFRACTIONr_nbd_refined0.3440.3107
X-RAY DIFFRACTIONr_nbd_other0.2220.3305
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2860.519
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.5501
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4230.336
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4190.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2541.5195
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3232312
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1283146
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.8674.5144
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 44
Rwork0.199 769

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