+Open data
-Basic information
Entry | Database: PDB / ID: 1rhz | ||||||
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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: 3.5 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, 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 | 1rhz.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rhz.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rhz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rhz_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
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Full document | 1rhz_full_validation.pdf.gz | 490.4 KB | Display | |
Data in XML | 1rhz_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 1rhz_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/1rhz ftp://data.pdbj.org/pub/pdb/validation_reports/rh/1rhz | HTTPS FTP |
-Related 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: 47482.891 Da / Num. of mol.: 1 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: 4.44 Å3/Da / Density % sol: 72.32 % | ||||||||||||||||||||||||
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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: NSLS / Beamline: X25 / Wavelength: 0.9799 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2002 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→10 Å / Num. all: 13799 / Num. obs: 13601 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.08 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 3.5→3.7 Å / Mean I/σ(I) obs: 2.74 / Num. unique all: 2010 / Rsym value: 0.67 / % possible all: 92.5 |
Reflection | *PLUS Num. obs: 14439 / % possible obs: 98.4 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 3.63 Å / % possible obs: 89.6 % / Num. unique obs: 1291 / Rmerge(I) obs: 0.67 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.5→9.99 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 845652.81 / Data cutoff high rms absF: 845652.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 79.707 Å2 / ksol: 0.272543 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 122.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.71 Å / Rfactor Rfree error: 0.047 / 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 Highest resolution: 3.5 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.334 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 3.63 Å |