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Yorodumi- PDB-1cwq: M INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cwq | |||||||||
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Title | M INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN COMBINATION WITH THE GROUND STATE STRUCTURE | |||||||||
Components | BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE) | |||||||||
Keywords | ION TRANSPORT / PHOTO CYCLE INTERMEDIATE / 7-HELICAL MEMBRANE PROTEIN / PROTON TRANSPORT / RETINAL PROTEIN | |||||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Halobacterium salinarum (Halophile) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Sass, H.J. / Berendzen, J. / Neff, D. / Gessenich, R. / Ormos, P. / Bueldt, G. | |||||||||
Citation | Journal: Nature / Year: 2000 Title: Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin. Authors: Sass, H.J. / Buldt, G. / Gessenich, R. / Hehn, D. / Neff, D. / Schlesinger, R. / Berendzen, J. / Ormos, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cwq.cif.gz | 117.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cwq.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/1cwq ftp://data.pdbj.org/pub/pdb/validation_reports/cw/1cwq | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26888.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SCHIFF BASE LINKAGE BETWEEN LYS 216 (NZ) AND RET 601 (C15) DIETHER LIPID BILAYER Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: TRANSMEMBRANETransmembrane protein / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945 |
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-Non-polymers , 6 types, 198 molecules
#2: Chemical | #3: Chemical | ChemComp-UND / #4: Chemical | ChemComp-OCT / #5: Chemical | ChemComp-HEX / #6: Chemical | ChemComp-TRD / #7: Water | ChemComp-HOH / | |
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-Details
Compound details | THE ENTRY CONTAINS THE COORDINATES OF THE M INTERMEDIATE (CHAIN B + LIPID RESIDUES 1604-1624 AND ...THE ENTRY CONTAINS THE COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Description: TWINNING OF 38% | |||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: CUBIC LIPID PHASE 2.5M PHOSPHATE, pH 5.60 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.6 / Method: cubic lipid phaseDetails: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532. | |||||||||||||||||||||||||
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: X8C / Wavelength: 1.214 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 9, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.214 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 10792 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 22.16 Å2 / Rsym value: 8.2 / Net I/σ(I): 12.05 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.4 / Rsym value: 32.8 / % possible all: 99.4 |
Reflection | *PLUS Rmerge(I) obs: 0.082 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→13 Å / Cross valid method: FREE R VALUE, MAXIMUM LIKELIHOOD / σ(F): 1 / Stereochemistry target values: ENGH & HUBER Details: THE TWIN RATIO OF 0.38 WAS CONSTANT DURING THE REFINEMENT.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 138.6 Å2 / ksol: 0.264 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.33 Å / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 13 Å / % reflection Rfree: 5.3 % / Rfactor obs: 0.179 / Rfactor Rfree: 0.208 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.293 / Rfactor Rwork: 0.195 |