[English] 日本語
Yorodumi- PDB-6pfp: Crystal Structure of Amino Acids 1473-1536 of Human Beta Cardiac ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pfp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Amino Acids 1473-1536 of Human Beta Cardiac Myosin Fused to Gp7 and Eb1 | ||||||
Components | Myosin-7 fused to GP7 and EB1 | ||||||
Keywords | MOTOR PROTEIN / Myosin Rod / Myosin / Coiled-Coil / Gp7 / Eb1 | ||||||
Function / homology | Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / viral scaffold / EB1-like C-terminal motif / virion assembly / DNA binding / Capsid assembly scaffolding protein Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Andreas, M.P. / Korkmaz, E.N. / Kirsch, C.J. / Hargreaves, M.D. / Kieffer, D.J. / Ajay, G. / Cui, Q. / Rayment, I. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: A Complete Model of the Cardiac Myosin Rod Authors: Andreas, M.P. / Korkmaz, E.N. / Kirsch, C.J. / Hargreaves, M. / Kieffer, D.J. / Ajay, G. / Cui, Q. / Rayment, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6pfp.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6pfp.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 6pfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/6pfp ftp://data.pdbj.org/pub/pdb/validation_reports/pf/6pfp | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19195.182 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYH7, MYHCB / Production host: Escherichia coli (E. coli) / References: UniProt: P13848*PLUS #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.26 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Crystals grew from 1:1 mixture of 18 mg/ml protein solution with 37% (w/v) 2-methyl-2,4-pentanediol (MPD), 80 mM magnesium sulfate, 100 mM sodium acetate. Protein solution contained 10 mM 4- ...Details: Crystals grew from 1:1 mixture of 18 mg/ml protein solution with 37% (w/v) 2-methyl-2,4-pentanediol (MPD), 80 mM magnesium sulfate, 100 mM sodium acetate. Protein solution contained 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) pH 7.6, and 0.2 mM tris(2-carboxyethyl)phosphine (TCEP). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 8, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 35454 / % possible obs: 95.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.05 / Rrim(I) all: 0.106 / Χ2: 0.857 / Net I/σ(I): 7.1 / Num. measured all: 128524 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INOH Resolution: 2.2→37.177 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.01
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.99 Å2 / Biso mean: 41.3123 Å2 / Biso min: 7.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→37.177 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
|