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Yorodumi- PDB-5yjl: Crystal structure of Arabidopsis glutamyl-tRNA reductase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yjl | ||||||
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Title | Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with NADPH and GBP | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / GTR / ALA / tetrapyrrole | ||||||
Function / homology | Function and homology information glutamyl-tRNA reductase / glutamyl-tRNA reductase activity / tetrapyrrole biosynthetic process / positive regulation of heme biosynthetic process / chloroplast membrane / chlorophyll biosynthetic process / chloroplast thylakoid / protoporphyrinogen IX biosynthetic process / photosynthetic electron transport chain / heme biosynthetic process ...glutamyl-tRNA reductase / glutamyl-tRNA reductase activity / tetrapyrrole biosynthetic process / positive regulation of heme biosynthetic process / chloroplast membrane / chlorophyll biosynthetic process / chloroplast thylakoid / protoporphyrinogen IX biosynthetic process / photosynthetic electron transport chain / heme biosynthetic process / chloroplast stroma / protein-membrane adaptor activity / post-embryonic development / chloroplast / NADP binding / protein-containing complex Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Zhao, A. / Han, F. | ||||||
Funding support | China, 1items
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Citation | Journal: Photosyn. Res. / Year: 2018 Title: Crystal structure of Arabidopsis thaliana glutamyl-tRNAGlureductase in complex with NADPH and glutamyl-tRNAGlureductase binding protein Authors: Zhao, A. / Han, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yjl.cif.gz | 277 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yjl.ent.gz | 218.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yjl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5yjl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5yjl_validation.xml.gz | 51.5 KB | Display | |
Data in CIF | 5yjl_validation.cif.gz | 72 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/5yjl ftp://data.pdbj.org/pub/pdb/validation_reports/yj/5yjl | HTTPS FTP |
-Related structure data
Related structure data | 4n7rS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52139.902 Da / Num. of mol.: 2 / Fragment: UNP residues 73-543 Source method: isolated from a genetically manipulated source Details: NAP / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HEMA1 / Plasmid: PMAL-C5X / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42804, glutamyl-tRNA reductase #2: Protein | Mass: 34272.648 Da / Num. of mol.: 2 / Fragment: UNP residues 42-317 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PGR7 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LU39 #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: 2.52 Å3/Da / Density % sol: 51.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 22.5%(w/v) PEG 3,350, 0.3M ammonium citrate tribasic, pH 7.0, 0.4mM NADPH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2013 |
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→32.958 Å / Num. obs: 48449 / % possible obs: 98.8 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.687 / Rsym value: 0.687 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N7R Resolution: 2.7→32.958 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→32.958 Å
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Refine LS restraints |
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LS refinement shell |
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