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Yorodumi- PDB-3aek: Structure of the light-independent protochlorophyllide reductase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aek | ||||||
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Title | Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Iron/sulfur cluster / Bacteriochlorophyll biosynthesis / Chlorophyll biosynthesis / Photosynthesis | ||||||
Function / homology | Function and homology information ferredoxin:protochlorophyllide reductase (ATP-dependent) / photosynthesis, dark reaction / light-independent bacteriochlorophyll biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / oxidoreductase activity, acting on iron-sulfur proteins as donors / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Muraki, N. / Nomata, J. / Shiba, T. / Fujita, Y. / Kurisu, G. | ||||||
Citation | Journal: Nature / Year: 2010 Title: X-ray crystal structure of the light-independent protochlorophyllide reductase Authors: Muraki, N. / Nomata, J. / Ebata, K. / Mizoguchi, T. / Shiba, T. / Tamiaki, H. / Kurisu, G. / Fujita, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aek.cif.gz | 346.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aek.ent.gz | 274 KB | Display | PDB format |
PDBx/mmJSON format | 3aek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/3aek ftp://data.pdbj.org/pub/pdb/validation_reports/ae/3aek | HTTPS FTP |
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-Related structure data
Related structure data | 3aeqC 3aerC 3aesC 3aetC 3aeuC 2zmp C: citing same article (ref.) 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
#1: Protein | Mass: 47284.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: bchN / Plasmid: PBBR1MCS2 / Production host: rhodobacter capsulatus (bacteria) / References: UniProt: P26164, EC: 1.18.-.- #2: Protein | Mass: 57261.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: bchB, bchK / Plasmid: PBBR1MCS2 / Production host: rhodobacter capsulatus (bacteria) / References: UniProt: P26163, EC: 1.18.-.- #3: Chemical | #4: Chemical | #5: 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: 2.78 Å3/Da / Density % sol: 55.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 16% PEG4000, 0.2M SODIUM/POTASSIUM PHOSPHATE(PH5.0), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 100467 / % possible obs: 99.9 % / Observed criterion σ(I): -2 / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZMP 2zmp Resolution: 2.3→34.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.279 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 37.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→34.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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