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Yorodumi- PDB-2zbf: Calcium pump crystal structure with bound BeF3 and TG in the abse... -
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-Basic information
Entry | Database: PDB / ID: 2zbf | ||||||
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Title | Calcium pump crystal structure with bound BeF3 and TG in the absence of calcium | ||||||
Components | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | ||||||
Keywords | HYDROLASE / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / ATP-BINDING / CALCIUM TRANSPORT / ENDOPLASMIC RETICULUM / ION TRANSPORT / MAGNESIUM / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SARCOPLASMIC RETICULUM / TRANSMEMBRANE / TRANSPORT | ||||||
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 / positive regulation of ATPase-coupled calcium transmembrane transporter activity / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / 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 / positive regulation of ATPase-coupled calcium transmembrane transporter activity / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / 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 | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Toyoshima, C. / Ogawa, H. / Norimatsu, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump Authors: Toyoshima, C. / Norimatsu, Y. / Iwasawa, S. / Tsuda, T. / Ogawa, 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: 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 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. #6: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zbf.cif.gz | 214.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zbf.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/2zbf ftp://data.pdbj.org/pub/pdb/validation_reports/zb/2zbf | HTTPS FTP |
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-Related structure data
Related structure data | 2zbeC 2zbgC 1wpgS 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: 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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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-BEF / |
#4: Chemical | ChemComp-TG1 / |
#5: Water | ChemComp-HOH / |
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. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.07 % |
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Crystal grow | Temperature: 283 K / Method: microdialysis / pH: 5.7 / Details: pH 5.7, MICRODIALYSIS, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2007 |
Radiation | Monochromator: ROTATED-INCLINED DOUBLE- CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 52437 / Num. obs: 50077 / % possible obs: 95.5 % / Observed criterion σ(I): -2 / Redundancy: 6.8 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2445 / % possible all: 79.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WPG Resolution: 2.4→11.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2327710.91 / 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: 73.8718 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→11.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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