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- PDB-3uf1: Crystal Structure of Vimentin (fragment 144-251) from Homo sapien... -

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Basic information

Entry
Database: PDB / ID: 3uf1
TitleCrystal Structure of Vimentin (fragment 144-251) from Homo sapiens, Northeast Structural Genomics Consortium Target HR4796B
ComponentsVimentin
KeywordsSTRUCTURAL PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / VIM / Intermediate filaments (IF) / filamentous cytoskeleton
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 / RHOBTB1 GTPase cycle / microtubule organizing center / 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 / RHOBTB1 GTPase cycle / microtubule organizing center / 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
: / 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 / SAD / Resolution: 2.81 Å
AuthorsKuzin, A. / Abashidze, M. / Vorobiev, S.M. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Abashidze, M. / Vorobiev, S.M. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The structure of vimentin linker 1 and rod 1B domains characterized by site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) and X-ray crystallography.
Authors: Aziz, A. / Hess, J.F. / Budamagunta, M.S. / Voss, J.C. / Kuzin, A.P. / Huang, Y.J. / Xiao, R. / Montelione, G.T. / FitzGerald, P.G. / Hunt, J.F.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionNov 30, 2011ID: 3OL1
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references

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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


Theoretical massNumber of molelcules
Total (without water)58,5544
Polymers58,5544
Non-polymers00
Water00
1
A: Vimentin
B: Vimentin


Theoretical massNumber of molelcules
Total (without water)29,2772
Polymers29,2772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-60 kcal/mol
Surface area15320 Å2
MethodPISA
2
C: Vimentin
D: Vimentin


Theoretical massNumber of molelcules
Total (without water)29,2772
Polymers29,2772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-64 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.017, 86.810, 114.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B and (resseq 146:248 )
211chain D and (resseq 146:248 )
112chain A and (resseq 147:246 )
212chain C and (resseq 147:246 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
Vimentin


Mass: 14638.472 Da / Num. of mol.: 4 / Fragment: residues 144-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VIM / References: UniProt: P08670

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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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution:NH4SO4 0.15M, TRISHCL 0.1M, PEG3350 18%, VAPOR DIFFUSION, HANGING DROP,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2010 / Details: MIRROR
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 28240 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 22.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3 / % possible all: 93

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→19.803 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.73 / σ(F): 1.34 / Phase error: 33.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 1496 9.85 %
Rwork0.2336 --
obs0.2387 15190 98.74 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.786 Å2 / ksol: 0.302 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-22.8175 Å20 Å2-0 Å2
2--4.0085 Å20 Å2
3----26.826 Å2
Refinement stepCycle: LAST / Resolution: 2.81→19.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 0 0 3639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093660
X-RAY DIFFRACTIONf_angle_d1.0814888
X-RAY DIFFRACTIONf_dihedral_angle_d19.9991504
X-RAY DIFFRACTIONf_chiral_restr0.068533
X-RAY DIFFRACTIONf_plane_restr0.002670
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B867X-RAY DIFFRACTIONPOSITIONAL
12D867X-RAY DIFFRACTIONPOSITIONAL0.049
21A845X-RAY DIFFRACTIONPOSITIONAL
22C845X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8102-2.90060.39981500.34141069X-RAY DIFFRACTION89
2.9006-3.00390.3779750.31691287X-RAY DIFFRACTION99
3.0039-3.12380.37711500.31531216X-RAY DIFFRACTION99
3.1238-3.26530.35471490.28241223X-RAY DIFFRACTION100
3.2653-3.43670.31991500.28481223X-RAY DIFFRACTION100
3.4367-3.65070.32151500.26541242X-RAY DIFFRACTION100
3.6507-3.93060.2934750.22281319X-RAY DIFFRACTION100
3.9306-4.32240.21151500.18521237X-RAY DIFFRACTION100
4.3224-4.93940.25091490.18431257X-RAY DIFFRACTION100
4.9394-6.19140.29791480.24851277X-RAY DIFFRACTION99
6.1914-19.80320.23991500.19451344X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 82.9187 Å / Origin y: 81.7854 Å / Origin z: 119.7951 Å
111213212223313233
T0.1772 Å2-0.0899 Å20.0264 Å2-0.2717 Å2-0.0846 Å2--0.2643 Å2
L0.1229 °20.2607 °20.3901 °2-0.7412 °20.1622 °2--1.1224 °2
S0.0261 Å °0.0531 Å °-0.1414 Å °-0.1993 Å °0.1761 Å °-0.1016 Å °0.3326 Å °0.5859 Å °-0.0149 Å °
Refinement TLS groupSelection details: all

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