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Yorodumi- PDB-2i5n: 1.96 A X-ray structure of photosynthetic reaction center from Rho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i5n | ||||||
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Title | 1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas viridis:Crystals grown by microfluidic technique | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosynthetic reaction center / secondary quinone (QB) / microfluidic technique / hybrid / microbatch / plug | ||||||
Function / homology | Function and homology information plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Blastochloris viridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Li, L. / Mustafi, D. / Fu, Q. / Tereshko, V. / Chen, D.L. / Tice, J.D. / Ismagilov, R.F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins. Authors: Li, L. / Mustafi, D. / Fu, Q. / Tereshko, V. / Chen, D.L. / Tice, J.D. / Ismagilov, R.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i5n.cif.gz | 297.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i5n.ent.gz | 233.2 KB | Display | PDB format |
PDBx/mmJSON format | 2i5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i5n_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2i5n_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2i5n_validation.xml.gz | 57.9 KB | Display | |
Data in CIF | 2i5n_validation.cif.gz | 81.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/2i5n ftp://data.pdbj.org/pub/pdb/validation_reports/i5/2i5n | HTTPS FTP |
-Related structure data
Related structure data | 1dxrS 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, 1 molecules C
#1: Protein | Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: INTRACYTOPLASMIC MEMBRANE (ICM) / References: UniProt: P07173 |
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-Reaction center protein ... , 3 types, 3 molecules HLM
#2: Protein | Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: INTRACYTOPLASMIC MEMBRANE (ICM) / References: UniProt: P06008 |
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#3: Protein | Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: INTRACYTOPLASMIC MEMBRANE (ICM) / References: UniProt: P06009 |
#4: Protein | Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: INTRACYTOPLASMIC MEMBRANE (ICM) / References: UniProt: P06010 |
-Non-polymers , 12 types, 820 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-HEC / #7: Chemical | ChemComp-HTO / #8: Chemical | ChemComp-LDA / #9: Chemical | ChemComp-UNL / Num. of mol.: 6 / Source method: obtained synthetically #10: Chemical | ChemComp-FE2 / | #11: Chemical | ChemComp-BCB / #12: Chemical | #13: Chemical | ChemComp-MQ9 / | #14: Chemical | #15: Chemical | ChemComp-NS5 / | #16: 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: 5 Å3/Da / Density % sol: 70 % |
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Crystal grow | Details: THE CRYSTALS WERE GROWN BY MICROFLUIDIC TECHNIQUE USING CRYSTALLIZATION BUFFER: 1.6 - 1.8 M (NH4)2SO4 IN TRIS PH 7.8. THE ADDITIVES WERE HEPTANETRIOL (3%, W/V) AND 2% TRIETHYL AMONIUM ...Details: THE CRYSTALS WERE GROWN BY MICROFLUIDIC TECHNIQUE USING CRYSTALLIZATION BUFFER: 1.6 - 1.8 M (NH4)2SO4 IN TRIS PH 7.8. THE ADDITIVES WERE HEPTANETRIOL (3%, W/V) AND 2% TRIETHYL AMONIUM PHOSPHATE. THE DETERGENT WAS LAURYL DIMETHYLAMINE-N-OXIDE (LDA). THE PROTEIN COMPLEX WAS IN SODIUM PHOSPHATE BUFFER PH 6.0 AND 0.08% LDA. |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 17, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→20 Å / Num. obs: 189189 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.96→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.3 / % possible all: 67.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DXR Resolution: 1.96→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.071 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BOTH AMMONIUM SULFATE AND PHOSPHATE BUFFER WERE USED IN THE CRYSTALLIZATION, THEREFORE SOME OF SO4 IONS (U 801-813) IDENTIFIED IN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BOTH AMMONIUM SULFATE AND PHOSPHATE BUFFER WERE USED IN THE CRYSTALLIZATION, THEREFORE SOME OF SO4 IONS (U 801-813) IDENTIFIED IN THE STRUCTURE COULD BE PHOSPHATE IONS. DIFFERENCE ELECTRON DENSITY WAS DETECTED AT >2.5 SIGMA LEVEL NEXT TO SEVERAL LYS (L 207) AND HIS (C 24, M 16, M 78, M 108, M 143) RESIDUES. THESE SITES WERE INCORPORATED IN THE COORDINATE FILES AS SO4 RESIDUES (U 814-819) WITH OCCUPANCY=0. SEVERAL REGIONS DISPLAYED TUBE-LIKE DIFFERENCE DENSITY AT THE SURFACE OF THE COMPLEX. WE HAVE USED DETERGENT IN THE CRYSTALLIZATION AND PARAFFIN OIL FOR CRYO-PROTECTION. THE DIFFERENCE DENSITY WAS DETECTED ONLY AT 2.5 SIGMA LEVEL INDICATING THAT THESE SITES ARE ONLY PARTIALLY OCCUPIED. THE DIFFERENCE DENSITY HAS BEEN TREATED AS AN UNKNOWN LIGAND TYPE (UNL) WITH OCCUPANCY=0.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.02 Å / Total num. of bins used: 20
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