+Open data
-Basic information
Entry | Database: PDB / ID: 1rh5 | ||||||
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Title | The structure of a protein conducting channel | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Protein translocation / SecY / Membrane Protein / Protein Channels | ||||||
Function / homology | Function and homology information intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / protein transport / plasma membrane Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | ||||||
Authors | van den Berg, B. / Clemons Jr., W.M. / Collinson, I. / Modis, Y. / Hartmann, E. / Harrison, S.C. / Rapoport, T.A. | ||||||
Citation | Journal: Nature / Year: 2004 Title: X-ray structure of a protein-conducting channel Authors: van den Berg, B. / Clemons Jr., W.M. / Collinson, I. / Modis, Y. / Hartmann, E. / Harrison, S.C. / Rapoport, T.A. | ||||||
History |
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Remark 999 | sequence No suitable sequence database reference was available for chain C at the time of ...sequence No suitable sequence database reference was available for chain C at the time of processing this file. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rh5.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rh5.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/1rh5 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/1rh5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Biological assembly consists of a tetramer. |
-Components
#1: Protein | Mass: 47512.879 Da / Num. of mol.: 1 / Mutation: R422K, T423V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: SECY, MJ0478 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q60175 |
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#2: Protein | Mass: 8451.144 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: SECE, MJ0371 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q57817 |
#3: Protein | Mass: 5967.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P60460*PLUS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.54 Å3/Da / Density % sol: 72.93 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: Peg 400, Glycine buffer, glycerol, sodium chloride, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 9.5 / PH range high: 9 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 1, 2003 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→10 Å / Num. all: 18818 / Num. obs: 17396 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.05 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2.24 / Num. unique all: 1439 / Rsym value: 0.44 / % possible all: 76.1 |
Reflection | *PLUS Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Highest resolution: 3.2 Å / % possible obs: 76.1 % / Num. unique obs: 1439 / Rmerge(I) obs: 0.44 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.2→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 348802.96 / Data cutoff high rms absF: 348802.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.7652 Å2 / ksol: 0.309755 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.39 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.287 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 3.31 Å / Rfactor Rfree: 0.442 / Rfactor Rwork: 0.414 |