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Yorodumi- PDB-2zxl: Crystal structure of red chlorophyll catabolite reductase from Ar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zxl | ||||||
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Title | Crystal structure of red chlorophyll catabolite reductase from Arabidopsis thaliana | ||||||
Components | Red chlorophyll catabolite reductase, chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / ALPHA-BETA-ALPHA SANDWICH / Chlorophyll catabolism / Chloroplast / Coiled coil / NADP / Plastid / Transit peptide | ||||||
Function / homology | Function and homology information red chlorophyll catabolite reductase / red chlorophyll catabolite reductase activity / chlorophyll catabolic process / regulation of plant-type hypersensitive response / defense response to other organism / regulation of programmed cell death / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast ...red chlorophyll catabolite reductase / red chlorophyll catabolite reductase activity / chlorophyll catabolic process / regulation of plant-type hypersensitive response / defense response to other organism / regulation of programmed cell death / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / mitochondrion / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sugishima, M. / Kitamori, Y. / Fukuyama, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structure of red chlorophyll catabolite reductase: enlargement of the ferredoxin-dependent bilin reductase family Authors: Sugishima, M. / Kitamori, Y. / Noguchi, M. / Kohchi, T. / Fukuyama, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zxl.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zxl.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/2zxl ftp://data.pdbj.org/pub/pdb/validation_reports/zx/2zxl | HTTPS FTP |
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-Related structure data
Related structure data | 2zxkSC S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 55 - 318 / Label seq-ID: 21 - 284
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-Components
#1: Protein | Mass: 32477.910 Da / Num. of mol.: 2 / Fragment: truncated the chloroplast transit peptide Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RCCR / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q8LDU4, EC: 1.3.1.80 #2: Chemical | #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: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25% PEG 4000, 0.1M ammonium sulfate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING 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: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2007 |
Radiation | Monochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 22833 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3315 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZXK Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.887 / SU B: 24.211 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.579 / ESU R Free: 0.332 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1934 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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