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Yorodumi- PDB-3aer: Structure of the light-independent protochlorophyllide reductase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aer | ||||||
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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: 2.8 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 | 3aer.cif.gz | 330.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aer.ent.gz | 262.6 KB | Display | PDB format |
PDBx/mmJSON format | 3aer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aer_validation.pdf.gz | 485.7 KB | Display | wwPDB validaton report |
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Full document | 3aer_full_validation.pdf.gz | 520.3 KB | Display | |
Data in XML | 3aer_validation.xml.gz | 59.2 KB | Display | |
Data in CIF | 3aer_validation.cif.gz | 82.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/3aer ftp://data.pdbj.org/pub/pdb/validation_reports/ae/3aer | HTTPS FTP |
-Related structure data
Related structure data | 3aekC 3aeqC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 6
NCS ensembles :
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-Components
#1: Protein | Mass: 47212.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: bchN / Plasmid: PASK-IBA5PLUS / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / 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: PASK-IBA5PLUS / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P26163, EC: 1.18.-.- #3: Chemical | #4: 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: 2.77 Å3/Da / Density % sol: 55.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG3350, 0.2M AMMONIUM CLORIDE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 51405 / % possible obs: 92 % / Observed criterion σ(I): -2 / Biso Wilson estimate: 55.83 Å2 / Rmerge(I) obs: 0.106 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZMP 2zmp Resolution: 2.8→47.09 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 27.328 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / 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: 41.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→47.09 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.87 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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