+Open data
-Basic information
Entry | Database: PDB / ID: 3a7k | ||||||
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Title | Crystal structure of halorhodopsin from Natronomonas pharaonis | ||||||
Components | Halorhodopsin | ||||||
Keywords | MEMBRANE PROTEIN / Light-driven chloride ion pump / Trimeric Bacterioruberin-Protein Complex / Retinal Protein | ||||||
Function / homology | Function and homology information Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Natronomonas pharaonis DSM 2160 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kouyama, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis. Authors: Kouyama, T. / Kanada, S. / Takeguchi, Y. / Narusawa, A. / Murakami, M. / Ihara, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a7k.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a7k.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 3a7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a7k_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 3a7k_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 3a7k_validation.xml.gz | 42 KB | Display | |
Data in CIF | 3a7k_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/3a7k ftp://data.pdbj.org/pub/pdb/validation_reports/a7/3a7k | HTTPS FTP |
-Related structure data
Related structure data | 1e12S 3a4b S: Starting model for refinement |
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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, 3 molecules ABD
#1: Protein | Mass: 30975.096 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: STRAIN MK-1 WAS A HALORHODOPSIN-OVERPRODUCING MUTANT GENERATED FROM TYPE STRAIN D2160T. Source: (natural) Natronomonas pharaonis DSM 2160 (archaea) / References: UniProt: Q3ITX1 |
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-Non-polymers , 7 types, 174 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-L2P / #6: Chemical | ChemComp-L3P / #7: Chemical | ChemComp-CL / #8: Water | ChemComp-HOH / | |
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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: 3.2 Å3/Da / Density % sol: 61.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: A DROP CONTAINING 1MG/ML PROTEIN, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, 0.04% NAN2, 5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVE SOLUTION ...Details: A DROP CONTAINING 1MG/ML PROTEIN, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, 0.04% NAN2, 5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVE SOLUTION CONTAINING 2.6 M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, PH 8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2009 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→60.1 Å / Num. obs: 79092 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2 / Rsym value: 0.556 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1e12 Resolution: 2→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 109.866 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.222 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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