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- PDB-2zbd: Crystal Structure of the SR Calcium Pump with Bound Aluminium Flu... -
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Basic information
Entry | Database: PDB / ID: 2zbd | |||||||||
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Title | Crystal Structure of the SR Calcium Pump with Bound Aluminium Fluoride, ADP and Calcium | |||||||||
![]() | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | |||||||||
![]() | HYDROLASE / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / ALTERNATIVE SPLICING / ATP-BINDING / CALCIUM / CALCIUM TRANSPORT / ENDOPLASMIC RETICULUM / ION TRANSPORT / MAGNESIUM / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SARCOPLASMIC RETICULUM / TRANSMEMBRANE / 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 | ![]() ![]() ![]() | |||||||||
![]() | Toyoshima, C. / Nomura, H. / Tsuda, T. / Ogawa, H. / Norimatsu, Y. | |||||||||
![]() | ![]() Title: Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues Authors: Toyoshima, C. / Nomura, H. / Tsuda, T. #1: ![]() 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: ![]() Title: Structural changes in the calcium pump accompanying the dissociation of calcium Authors: Toyoshima, C. / Nomura, H. #3: ![]() Title: Crystal structure of the calcium pump with a bound ATP analogue Authors: Toyoshima, C. / Mizutani, T. #4: ![]() Title: Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+) Authors: Obara, K. / Miyashita, N. / Xu, C. / Toyoshima, I. / Sugita, Y. / Inesi, G. / Toyoshima, C. #5: ![]() Title: Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors Authors: Takahashi, M. / Kondou, Y. / Toyoshima, C. | |||||||||
History |
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Remark 999 | SEQUENCE The C-terminal residues in UNP entry P04191 are from 994 to 1001, DPEDERRK. In isoform ...SEQUENCE 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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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.9 KB | Display | ![]() |
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PDB format | ![]() | 164.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 530.6 KB | Display | ![]() |
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Full document | ![]() | 544.8 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wpgC ![]() 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
-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) ![]() ![]() |
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-Non-polymers , 6 types, 106 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ALF / | #5: Chemical | ChemComp-ADP / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.29 % |
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Crystal grow | Temperature: 283 K / pH: 6.1 / Details: PEG 400, pH 6.10, MICRODIALYSIS, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / 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: 2.4→20 Å / Num. obs: 61807 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 58.5 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WPE ![]() 1wpe Resolution: 2.4→12 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / SU B: 22.182 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.569 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Total num. of bins used: 20
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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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