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Yorodumi- PDB-3d38: Crystal structure of new trigonal form of photosynthetic reaction... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d38 | ||||||
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Title | Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture. | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / detergent extraction / reaction center / microfludics / plugs / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / Electron transport / Heme / Iron / Lipoprotein / Membrane / Metal-binding / Transport / Bacteriochlorophyll / Chlorophyll / Chromophore / Formylation / Transmembrane / Magnesium | ||||||
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: 3.21 Å | ||||||
Authors | Li, L. / Nachtergaele, S.H.M. / Seddon, A.M. / Tereshko, V. / Ponomarenko, N. / Ismagilov, R.F. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: Simple host-guest chemistry to modulate the process of concentration and crystallization of membrane proteins by detergent capture in a microfluidic device. Authors: Li, L. / Nachtergaele, S. / Seddon, A.M. / Tereshko, V. / Ponomarenko, N. / 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 | 3d38.cif.gz | 277.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d38.ent.gz | 218.5 KB | Display | PDB format |
PDBx/mmJSON format | 3d38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d38_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 3d38_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 3d38_validation.xml.gz | 57 KB | Display | |
Data in CIF | 3d38_validation.cif.gz | 74.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/3d38 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d38 | HTTPS FTP |
-Related structure data
Related structure data | 2i5nS 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) / 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) / 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) / 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) / References: UniProt: P06010 |
-Non-polymers , 11 types, 196 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-HEC / #7: Chemical | #8: Chemical | ChemComp-LDA / #9: Chemical | ChemComp-BCB / #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-FE2 / | #13: Chemical | ChemComp-MQ9 / | #14: Chemical | ChemComp-NS5 / | #15: 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: 7.19 Å3/Da / Density % sol: 82.9 % |
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Crystal grow | Temperature: 296 K / Method: plug-based microfluidics / pH: 6 Details: 9 mg/mL Protein, 4.6 mM LDAO, 10 mM Methyl-beta-cyclodextrin, 1.6-1.7 M Sulfate, 4.5% w/v Triethylammonium phosphate pH 6.0, 3% 1,2,3-heptanetriol, 30 mM NaH2PO4-Na2HPO4 pH 6.0, Plug-based ...Details: 9 mg/mL Protein, 4.6 mM LDAO, 10 mM Methyl-beta-cyclodextrin, 1.6-1.7 M Sulfate, 4.5% w/v Triethylammonium phosphate pH 6.0, 3% 1,2,3-heptanetriol, 30 mM NaH2PO4-Na2HPO4 pH 6.0, Plug-based Microfluidics, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 62037 / Num. obs: 62037 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 30.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2I5N Resolution: 3.21→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.871 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.479 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 67.435 Å2
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Refinement step | Cycle: LAST / Resolution: 3.21→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.21→3.29 Å / Total num. of bins used: 20
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