+Open data
-Basic information
Entry | Database: PDB / ID: 1iwo | ||||||
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Title | Crystal structure of the SR Ca2+-ATPase in the absence of Ca2+ | ||||||
Components | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD fold / HYDROLASE / 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: 3.1 Å | ||||||
Authors | Toyoshima, C. / Nomura, H. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Structural changes in the calcium pump accompanying the dissociation of calcium Authors: Toyoshima, C. / Nomura, H. #1: Journal: Nature / Year: 2000 Title: Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution Authors: Toyoshima, C. / Nakasako, M. / Nomura, H. / Ogawa, H. #2: Journal: Cryst.Res.Technol. / Year: 1986 Title: The crystal and molecular structure of the sesquiterpenoid silerin (trilobolide) Authors: Kutschabsky, L. / Kretschmer, R.-G. / Ripperger, H. #3: Journal: Fortschr.Chem.Org.Naturst. / Year: 1997 Title: Sesquiterpenoids from Thapsia species and medicinal chemistry of the thapsigargins Authors: Christensen, S.B. / Andersen, A. / Smitt, U.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iwo.cif.gz | 353.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iwo.ent.gz | 290.5 KB | Display | PDB format |
PDBx/mmJSON format | 1iwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/1iwo ftp://data.pdbj.org/pub/pdb/validation_reports/iw/1iwo | HTTPS FTP |
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-Related structure data
Related structure data | 1eul 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.00013, 3.0E-5), Vector: |
-Components
#1: Protein | Mass: 109602.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle (white) / References: UniProt: P04191, EC: 3.6.1.38 #2: Chemical | Sequence details | THE C-TERMINAL RESIDUES IN SWS ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, ...THE C-TERMINAL RESIDUES IN SWS ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, THERE IS ONLY ONE C-TERMINAL RESIDUE 994 G. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: microdialysis / pH: 6.1 Details: PEG 400, MES, EGTA, glycerol, magnesium chloride, pH 6.1, MICRODIALYSIS, temperature 283K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 10, 2000 |
Radiation | Monochromator: KARKPATRIC-BOETZE TYPE RH-COATED DOUBLE MIRROR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. all: 52421 / Num. obs: 51314 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3 / Num. unique all: 3985 / % possible all: 97.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 7.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: cytoplasmic domains of 1EUL 1eul Resolution: 3.1→15 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber / Details: strict NCS was assumed throughout
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.756 Å2 / ksol: 0.220167 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83 Å2
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Refine analyze | Luzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.57 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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