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Yorodumi- PDB-1avs: X-RAY CRYSTALLOGRAPHIC STUDY OF CALCIUM-SATURATED N-TERMINAL DOMA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1avs | ||||||
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Title | X-RAY CRYSTALLOGRAPHIC STUDY OF CALCIUM-SATURATED N-TERMINAL DOMAIN OF TROPONIN C | ||||||
Components | TROPONIN C | ||||||
Keywords | MUSCLE CONTRACTION / CALCIUM-ACTIVATED / TROPONIN / E-F HAND CALCIUM-BINDING PROTEIN | ||||||
Function / homology | Function and homology information troponin complex / Striated Muscle Contraction / skeletal muscle contraction / calcium ion binding Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR / Resolution: 1.75 Å | ||||||
Authors | Strynadka, N.C.J. / James, M.N.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Structural details of a calcium-induced molecular switch: X-ray crystallographic analysis of the calcium-saturated N-terminal domain of troponin C at 1.75 A resolution. Authors: Strynadka, N.C. / Cherney, M. / Sielecki, A.R. / Li, M.X. / Smillie, L.B. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avs.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avs.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 1avs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1avs_validation.pdf.gz | 379 KB | Display | wwPDB validaton report |
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Full document | 1avs_full_validation.pdf.gz | 386.7 KB | Display | |
Data in XML | 1avs_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1avs_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avs ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avs | HTTPS FTP |
-Related structure data
Related structure data | 4tncS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.694896, -0.010889, 0.719028), Vector: |
-Components
#1: Protein | Mass: 9984.085 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1 - 90 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Tissue: BREAST / Production host: Escherichia coli (E. coli) / References: UniProt: P02588 #2: Chemical | ChemComp-CA / #3: 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: 2.4 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 72 % AMMONIUM SULFATE 100 MM TRIS 2 % MPD, 5 MM CALCIUM CHLORIDE PH 7.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.009 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: NO MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 18010 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.104 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.75→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 3 / Rsym value: 0.28 / % possible all: 82 |
Reflection | *PLUS Num. measured all: 85689 |
Reflection shell | *PLUS % possible obs: 82 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, MIR Starting model: PDB ENTRY 4TNC Resolution: 1.75→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 300 Å2 / ksol: 0.75 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.214 / Rfactor Rfree: 0.251 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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