+Open data
-Basic information
Entry | Database: PDB / ID: 6k2f | ||||||
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Title | Structure of Eh TWINFILIN | ||||||
Components | Actin binding protein family protein | ||||||
Keywords | STRUCTURAL PROTEIN / Nt Twinfilin / Actin-Binding Protein | ||||||
Function / homology | Function and homology information negative regulation of actin filament polymerization / actin binding / cytoskeleton Similarity search - Function | ||||||
Biological species | Entamoeba histolytica HM-1:IMSS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Kumar, N. / Gourinath, S. / Rath, P.P. | ||||||
Citation | Journal: To Be Published Title: Structure of N-terminal Twinfilin domain from Entamoeba histolytica Authors: Kumar, N. / Gourinath, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k2f.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k2f.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 6k2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/6k2f ftp://data.pdbj.org/pub/pdb/validation_reports/k2/6k2f | HTTPS FTP |
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-Related structure data
Related structure data | 2vacS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15757.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote) Strain: HM-1:IMSS / Plasmid: pET 28(b) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: M3TR43, UniProt: N9V330*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.38 % / Description: Looks like Needle |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7.3 / Details: 25-35% PEG 3350, 100 mM HEPES, pH 7.3-7.7 / PH range: 7.3-7.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30.27 Å / Num. obs: 39360 / % possible obs: 99.76 % / Redundancy: 4.3 % / Biso Wilson estimate: 17.45 Å2 / CC1/2: 0.858 / Rmerge(I) obs: 0.64 / Rpim(I) all: 0.167 / Rrim(I) all: 0.6659 / Net I/σ(I): 86.04 |
Reflection shell | Resolution: 1.55→1.605 Å / Rmerge(I) obs: 1.249 / Mean I/σ(I) obs: 6.09 / Num. unique obs: 3875 / CC1/2: 0.625 / Rpim(I) all: 0.3325 / Rrim(I) all: 1.295 / % possible all: 99.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VAC Resolution: 1.55→30.27 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.294 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.074 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.548→1.588 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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