+Open data
-Basic information
Entry | Database: PDB / ID: 3ffv | ||||||
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Title | Crystal Structure Analysis of Syd | ||||||
Components | Protein syd | ||||||
Keywords | PROTEIN BINDING / Membrane / Translocon / SecYEG / Syd / Nanodisc / Cell inner membrane / Cell membrane | ||||||
Function / homology | Function and homology information regulation of protein-containing complex assembly / extrinsic component of cytoplasmic side of plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Maurus, R. / Brayer, G.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structure, Binding, and Activity of Syd, a SecY-interacting Protein Authors: Dalal, K. / Nguyen, N. / Alami, M. / Tan, J. / Moraes, T.F. / Lee, W.C. / Maurus, R. / Sligar, S.S. / Brayer, G.D. / Duong, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ffv.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ffv.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ffv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/3ffv ftp://data.pdbj.org/pub/pdb/validation_reports/ff/3ffv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20729.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A8U0 #2: Water | ChemComp-HOH / | |
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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: 2.71 Å3/Da / Density % sol: 54.65 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 0.8-1.0 M sodium citrate, 0.2 M sodium chloride, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9788 | ||||||||||||||||||
Detector | Type: MARMOSAIC 325 MM CCD MARMOSAIC 325 MM CCD / Detector: CCD / Date: Jun 9, 2007 Details: FLAT MIRROR (VERTICAL FOCUSING); SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HO RIZONTAL FOCUSING); FLAT MIRROR (VERTICAL FOCUSING); SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) | ||||||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 29401 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.068 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 8.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→41.9 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 25 Å2
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Refinement step | Cycle: LAST / Resolution: 2→41.9 Å
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