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Yorodumi- PDB-5xn5: Homo-dimer crystal structure of geranylgeranyl diphosphate syntha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xn5 | ||||||
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Title | Homo-dimer crystal structure of geranylgeranyl diphosphate synthases 1 from Oryza sativa | ||||||
Components | Os07g0580900 protein | ||||||
Keywords | TRANSFERASE / homo-dimer / lsu-lsu / OSGGPPS1 | ||||||
Function / homology | Function and homology information farnesyltranstransferase activity / prenyltransferase activity / isoprenoid biosynthetic process Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å | ||||||
Authors | Wang, C. / Zhou, F. / Lu, S. / Zhang, P. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: A recruiting protein of geranylgeranyl diphosphate synthase controls metabolic flux toward chlorophyll biosynthesis in rice Authors: Zhou, F. / Wang, C.Y. / Gutensohn, M. / Jiang, L. / Zhang, P. / Zhang, D. / Dudareva, N. / Lu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xn5.cif.gz | 230 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xn5.ent.gz | 186.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/5xn5 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/5xn5 | HTTPS FTP |
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-Related structure data
Related structure data | 5xn6C 5e8hS 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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-Components
#1: Protein | Mass: 32865.441 Da / Num. of mol.: 2 / Fragment: UNP residues 62-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: Os07g0580900, OJ1301_C12.3, OSNPB_070580900, P0453G03.27 Production host: Escherichia coli O103:H2 str. 12009 (bacteria) References: UniProt: Q7XI92 #2: 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: 2.25 Å3/Da / Density % sol: 45.37 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0 M sodium malonate, 20% PEG 3350, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9798 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Sep 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.1 Å / Num. obs: 39062 / % possible obs: 99.2 % / Redundancy: 4 % / Net I/σ(I): 19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E8H Resolution: 2.002→38.056 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.89 Å2 / Biso mean: 33.0425 Å2 / Biso min: 16.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.002→38.056 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 14.9781 Å / Origin y: 12.9069 Å / Origin z: 19.2809 Å
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Refinement TLS group |
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