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Yorodumi- PDB-5dqr: The crystal structure of Arabidopsis 7-hydroxymethyl chlorophyll ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dqr | ||||||
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Title | The crystal structure of Arabidopsis 7-hydroxymethyl chlorophyll a reductase (HCAR) | ||||||
Components | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / iron-sulfur flavoenzyme / HCAR / chlorophyll cycle | ||||||
Function / homology | Function and homology information 7-hydroxymethyl chlorophyll a reductase / chlorophyll cycle / 7-hydroxymethyl chlorophyll a reductase activity / chlorophyll metabolic process / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / iron-sulfur cluster binding / chloroplast / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Wang, X. / Liu, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Crystal Structure and Catalytic Mechanism of 7-Hydroxymethyl Chlorophyll a Reductase Authors: Wang, X. / Liu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dqr.cif.gz | 506.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dqr.ent.gz | 413.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dqr_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 5dqr_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 5dqr_validation.xml.gz | 101.3 KB | Display | |
Data in CIF | 5dqr_validation.cif.gz | 132.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/5dqr ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49068.238 Da / Num. of mol.: 6 / Fragment: UNP residues 26-462 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HCAR, HMCR, At1g04620, T1G11.13 / Production host: Escherichia coli (E. coli) References: UniProt: Q8GS60, 7-hydroxymethyl chlorophyll a reductase #2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-FAD / #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: 2.21 Å3/Da / Density % sol: 44.45 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M MgCl2, 0.1M Tris-HCl pH 8.5, 25%PEG3350(w/v), 3% EG(v/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 66528 / % possible obs: 99.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.079 / Rsym value: 0.052 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.3 / Rejects: 0 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→44.61 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.51 / Stereochemistry target values: ML Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.23 Å2 / Biso mean: 17.02 Å2 / Biso min: 0.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→44.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24
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