+Open data
-Basic information
Entry | Database: PDB / ID: 2rik | ||||||
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Title | I-band fragment I67-I69 from titin | ||||||
Components | Titin | ||||||
Keywords | STRUCTURAL PROTEIN / I-set Ig fold / poly-Ig linear array | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Marino, M. / von Castelmur, E. / Labeit, D. / Labeit, S. / Mayans, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: A regular pattern of Ig super-motifs defines segmental flexibility as the elastic mechanism of the titin chain Authors: von Castelmur, E. / Marino, M. / Svergun, D.I. / Kreplak, L. / Ucurum-Fotiadis, Z. / Konarev, P.V. / Urzhumtsev, A. / Labeit, D. / Labeit, S. / Mayans, O. #1: Journal: J.Muscle Res.Cell.Motil. / Year: 2005 Title: Poly-Ig tandems from I-band titin share extended domain arrangements irrespective of the distinct features of their modular constituents Authors: Marino, M. / Svergun, D.I. / Kreplak, L. / Konarev, P.V. / Maco, B. / Labeit, D. / Mayans, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rik.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rik.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 2rik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/2rik ftp://data.pdbj.org/pub/pdb/validation_reports/ri/2rik | HTTPS FTP |
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-Related structure data
Related structure data | 2rjmC 3b43C 1tlkS C: citing same article (ref.) 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: 31322.566 Da / Num. of mol.: 1 / Fragment: I67-I69 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta References: UniProt: O97791*PLUS, non-specific serine/threonine protein kinase |
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#2: Water | ChemComp-HOH / |
Sequence details | THE DATABASE SEQUENCE ENTRY COVERING THIS CONSTRUCT IS EMBL Y14852, RABBIT SOLEUS TITIN MRNA, BASES ...THE DATABASE SEQUENCE ENTRY COVERING THIS CONSTRUCT IS EMBL Y14852, RABBIT SOLEUS TITIN MRNA, BASES 12457-13296. THE CLOSEST HOMOLOG IS HUMAN TITIN SWISSPROT ENTRY Q8WZ42, RESIDUES 8137-84. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: pH 4.6, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19 Å / Num. obs: 41644 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.57 % / Biso Wilson estimate: 25.981 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.25 |
Reflection shell | Resolution: 1.6→1.62 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1312 / % possible all: 87.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: trimmed poly-Ala model of 1TLK Resolution: 1.6→18.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.014 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.022 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→18.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 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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