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Yorodumi- PDB-2c9m: Structure of (SR) Calcium-ATPase in the Ca2E1 state solved in a P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c9m | ||||||
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Title | Structure of (SR) Calcium-ATPase in the Ca2E1 state solved in a P1 crystal form. | ||||||
Components | SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 | ||||||
Keywords | HYDROLASE / CA2+-ATPASE / P-TYPE ATPASE / CATION PUMP / MEMBRANE PROTEIN / MODULATORY ATP / ATP-BINDING / CALCIUM TRANSPORT / ION TRANSPORT / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION | ||||||
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: 3 Å | ||||||
Authors | Lund Jensen, A.-M. / Sorensen, T.L.-M. / Olesen, C. / Moller, J.V. / Nissen, P. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Modulatory and Catalytic Modes of ATP Binding by the Calcium Pump Authors: Lund Jensen, A.-M. / Sorensen, T.L.-M. / Olesen, C. / Moller, J.V. / Nissen, P. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c9m.cif.gz | 388.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c9m.ent.gz | 314.4 KB | Display | PDB format |
PDBx/mmJSON format | 2c9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c9m ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c9m | HTTPS FTP |
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-Related structure data
Related structure data | 2c88C 2c8kC 2c8lC 1su4S 1wpe S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 109602.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Organ: MUSCLESkeletal muscle / Tissue: FAST TWITCH SKELETAL MUSCLE / References: UniProt: P04191, EC: 3.6.3.8 #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | |
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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 Å3/Da / Density % sol: 59.1 % Description: DATA FROM A DOUBLE CRYSTAL WERE MERGED INTO A SINGLE DATA SET. |
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Crystal grow | pH: 6.8 / Details: 14% PEG 6000, 400 MM CACL2, pH 6.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9504 |
Detector | Type: MARRESEACH / Detector: CCD / Date: Jan 13, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9504 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 41479 / % possible obs: 80 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3→3.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / % possible all: 40 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SU4 Resolution: 3→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1074116.68 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: FEW DISORDERED LOOP REGIONS WERE MODELED STEREOCHEMICALLY.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.1474 Å2 / ksol: 0.225736 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 1.37 Å2 / Rms dev position: 0.0345 Å / Weight Biso : 2 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
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Xplor file |
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