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Yorodumi- PDB-1dtl: CRYSTAL STRUCTURE OF CALCIUM-SATURATED (3CA2+) CARDIAC TROPONIN C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dtl | ||||||
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Title | CRYSTAL STRUCTURE OF CALCIUM-SATURATED (3CA2+) CARDIAC TROPONIN C COMPLEXED WITH THE CALCIUM SENSITIZER BEPRIDIL AT 2.15 A RESOLUTION | ||||||
Components | CARDIAC TROPONIN C | ||||||
Keywords | STRUCTURAL PROTEIN / helix-turn-helix | ||||||
Function / homology | Function and homology information cardiac Troponin complex / Striated Muscle Contraction / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / calcium-dependent protein binding / calcium ion binding Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Li, Y. / Love, M.L. / Putkey, J.A. / Cohen, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Bepridil opens the regulatory N-terminal lobe of cardiac troponin C. Authors: Li, Y. / Love, M.L. / Putkey, J.A. / Cohen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dtl.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dtl.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dtl ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dtl | HTTPS FTP |
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-Related 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: 18401.377 Da / Num. of mol.: 1 / Mutation: C35S, C84S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: P09860 | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG3350 monodisperse, magnesium chloride, calcium chloride, HEPES, bepridil, HCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.935 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 8025 / Num. obs: 7998 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.83 % / Biso Wilson estimate: 21.63 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.12 % / Rmerge(I) obs: 0.126 / Num. unique all: 764 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 54641 |
Reflection shell | *PLUS % possible obs: 99.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1AVS AND 1TN4 Resolution: 2.15→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.15→500 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.356 / % reflection Rfree: 4 % / Rfactor Rwork: 0.255 |