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Yorodumi- PDB-3ar6: Calcium pump crystal structure with bound TNP-ADP and TG in the a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ar6 | ||||||
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Title | Calcium pump crystal structure with bound TNP-ADP and TG in the absence of calcium | ||||||
Components | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / P-type ATPase / Hydrolase / Calcium Transport / Calcium Binding / ATP Binding / Endoplasmic Reticulum / SARCOPLASMIC RETICULUM / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / regulation of striated muscle contraction / negative regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type Ca2+ transporter / P-type calcium transporter activity ...positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / regulation of striated muscle contraction / negative regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / calcium ion transport / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Toyoshima, C. / Yonekura, S. / Tsueda, J. / Iwasawa, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca2+-ATPase in the absence of Ca2+. Authors: Toyoshima, C. / Yonekura, S. / Tsueda, J. / Iwasawa, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ar6.cif.gz | 218.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ar6.ent.gz | 170.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ar6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/3ar6 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/3ar6 | HTTPS FTP |
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-Related structure data
Related structure data | 3ar2C 3ar3C 3ar4C 3ar5C 3ar7C 3ar8C 3ar9C 1agvS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 109628.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Skeletal Muscle (white) / References: UniProt: P04191, EC: 3.6.3.8 |
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-Non-polymers , 6 types, 279 molecules
#2: Chemical | ChemComp-NA / | ||
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#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-TG1 / | ||
#5: Chemical | ChemComp-12D / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | UNP P04191 SHOWS THE RESUDIES 994-1001 DPEDERRK --> G IN ISOFORM SERCA1A AS NATURAL VARIATIONS |
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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: 3.44 Å3/Da / Density % sol: 64.24 % |
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Crystal grow | Temperature: 283 K / Method: microdialysis / pH: 6.1 / Details: pH 6.1, MICRODIALYSIS, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2007 |
Radiation | Monochromator: ROTATED-INCLINED DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 79615 / Num. obs: 78928 / % possible obs: 99.1 % / Observed criterion σ(I): -2 / Redundancy: 5.4 % / Biso Wilson estimate: 34.8 Å2 / Rsym value: 0.113 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.87 / Num. unique all: 5214 / Rsym value: 0.773 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AGV Resolution: 2.2→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3749258.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.26 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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