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- PDB-5xa7: Complete structure factors and an atomic model of the calcium pum... -
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Basic information
Entry | Database: PDB / ID: 5xa7 | ||||||
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Title | Complete structure factors and an atomic model of the calcium pump (SERCA1A) and associated phospholipids in the E1-2CA2+ crystals | ||||||
![]() | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | ||||||
![]() | HYDROLASE / P-TYPE ATPASE / CALCIUM TRANSPORT / CALCIUM BINDING / ENDOPLASMIC RETICULUM / SARCOPLASMIC RETICULUM / MET TRANSPORT | ||||||
Function / homology | ![]() 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 / negative regulation of striated muscle contraction / 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 / negative regulation of striated muscle contraction / 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 / intracellular calcium ion homeostasis / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Norimatsu, Y. / Hasegawa, K. / Shimizu, N. / Toyoshima, C. | ||||||
![]() | ![]() Title: Protein-phospholipid interplay revealed with crystals of a calcium pump. Authors: Norimatsu, Y. / Hasegawa, K. / Shimizu, N. / Toyoshima, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 425.9 KB | Display | ![]() |
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PDB format | ![]() | 342.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.1 MB | Display | ![]() |
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Full document | ![]() | 6.3 MB | Display | |
Data in XML | ![]() | 41.8 KB | Display | |
Data in CIF | ![]() | 56 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xa8C ![]() 5xa9C ![]() 5xaaC ![]() 5xabC ![]() 1wpe C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 109628.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-PCW / #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE OF THE PROTEIN WAS BASED ON ISOFORM 2 OF DATABASE UNP P04191. THE C-TERMINAL RESIDUES IN ...SEQUENCE OF THE PROTEIN WAS BASED ON ISOFORM 2 OF DATABASE UNP P04191. THE C-TERMINAL RESIDUES IN P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, THERE IS ONLY ONE C-TERMINAL RESIDUE 994 GLY. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.27 % |
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Crystal grow | Temperature: 283 K / Method: microdialysis / pH: 6.1 / Details: PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 13, 2005 |
Radiation | Monochromator: ROTATED-INCLINED DOUBLE- CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→144.75 Å / Num. obs: 25724 / % possible obs: 100 % / Redundancy: 1 % / Net I/σ(I): 81.76 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WPE ![]() 1wpe Resolution: 3.2→82.27 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.58 / Phase error: 24.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→82.27 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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