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Yorodumi- PDB-2c8k: Crystal Structure of (SR) Calcium-ATPase E2(Tg) with partially oc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c8k | ||||||
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Title | Crystal Structure of (SR) Calcium-ATPase E2(Tg) with partially occupied AMPPCP site | ||||||
Components | ARCOPLASMIC/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: 2.8 Å | ||||||
Authors | Jensen, A.M. / Sorensen, T.L. / 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: Jensen, A.M. / Sorensen, T.L. / 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 | 2c8k.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c8k.ent.gz | 163.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/2c8k ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c8k | HTTPS FTP |
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-Related structure data
Related structure data | 2c88C 2c8lC 2c9mC 1iwoS 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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Unit cell |
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-Components
#1: Protein | Mass: 109602.578 Da / Num. of mol.: 1 / 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 |
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#2: Chemical | ChemComp-TG1 / |
#3: Chemical | ChemComp-ACP / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-NA / |
Compound details | CATALYZES THE HYDROLYSIS OF ATP COUPLED WITH THE TRANSLOCATION OF CALCIUM FROM THE CYTOSOL TO THE ...CATALYZES THE HYDROLYSIS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63 % |
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Crystal grow | pH: 6.8 Details: 50 MM NAOAC, 15% PEG 2000 MME, 10% GLYCEROL, 4% MPD, pH 6.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.7 |
Detector | Type: MARRESEACH / Detector: IMAGE PLATE / Date: Sep 4, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 36358 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 62.8 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.8→3.01 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.6 / % possible all: 75.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IWO Resolution: 2.8→14.95 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2731058.53 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE AMPPCP OCCUPANCY WAS ESTIMATED TO 0.25 BY THE USE OG FOFC MAPS AND B FACTOR ANALYSIS. FEW DISORDERED LOOP REGIONS WERE MODELED STEREOCHEMICALLY.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.9276 Å2 / ksol: 0.296647 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→14.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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