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Yorodumi- PDB-2dqs: Crystal structure of the calcium pump with amppcp in the absence ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dqs | ||||||
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Title | Crystal structure of the calcium pump with amppcp in the absence of calcium | ||||||
Components | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | ||||||
Keywords | HYDROLASE / MEMBRANE PROTEIN / P-TYPE ATPASE / AMPPCP | ||||||
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: 2.5 Å | ||||||
Authors | Toyoshima, C. / Norimatsu, Y. / Tsueda, J. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the calcium pump with a bound ATP analogue in the absence of calcium Authors: Toyoshima, C. / Norimatsu, Y. / Tsueda, J. #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: Nature / Year: 2002 Title: Structural Changes in the Calcium Pump Accompanying the Dissociation of Calcium Authors: Toyoshima, C. / Nomura, H. #3: Journal: Nature / Year: 2004 Title: Crystal Structure of the Calcium Pump with a Bound ATP Analogue Authors: Toyoshima, C. / Mizutani, T. #4: Journal: Nature / Year: 2004 Title: Lumenal Gating Mechanism Revealed in Calcium Pump Crystal Structures with Phosphate Analogues Authors: Toyoshima, C. / Nomura, H. / Tsuda, T. #5: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Structural Role of Countertransport Revealed in Ca2+ Pump Crystal Structure in the Absence of Ca2+ Authors: Obara, K. / Miyashita, N. / Xu, C. / Toyoshima, I. / Sugita, Y. / Inesi, G. / Toyoshima, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dqs.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dqs.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 2dqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/2dqs ftp://data.pdbj.org/pub/pdb/validation_reports/dq/2dqs | HTTPS FTP |
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-Related structure data
Related structure data | 2agvS 1wpe 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, 239 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-ACP / | #5: Chemical | ChemComp-TG1 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE C-TERMINAL RESIDUES IN UNP ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, ...THE C-TERMINAL RESIDUES IN UNP ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, THERE IS ONLY ONE C-TERMINAL RESIDUE 994 GLY. |
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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: 3.43 Å3/Da / Density % sol: 64.15 % |
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Crystal grow | Temperature: 283 K / Method: microdialysis / pH: 6.1 / Details: pH 6.10, MICRODIALYSIS, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2006 |
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: 2.5→99 Å / Num. obs: 54985 / % possible obs: 99.6 % / Observed criterion σ(I): -2 / Redundancy: 8.8 % / Biso Wilson estimate: 50.3 Å2 / Rsym value: 0.083 / Net I/σ(I): 34.57 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.22 / Rsym value: 0.66 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AGV Resolution: 2.5→14.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3083694.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.8996 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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