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Yorodumi- PDB-2j1p: Geranylgeranyl diphosphate synthase from Sinapis alba in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j1p | ||||||
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Title | Geranylgeranyl diphosphate synthase from Sinapis alba in complex with GGPP | ||||||
Components | GERANYLGERANYL PYROPHOSPHATE SYNTHETASE | ||||||
Keywords | TRANSFERASE / ISOPRENE BIOSYNTHESIS / MULTIFUNCTIONAL ENZYME / CAROTENOID BIOSYNTHESIS / ISOPRENYL TRANSTRANSFERASE / ISOPRENOID DIPHOSPHATE SYNTHASE / TRANSIT PEPTIDE / CHLOROPLAST / GERANYLGERANYL DIPHOSPHATE | ||||||
Function / homology | Function and homology information chromoplast / carotenoid biosynthetic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase ...chromoplast / carotenoid biosynthetic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / chloroplast stroma / metal ion binding Similarity search - Function | ||||||
Biological species | SINAPIS ALBA (white mustard) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Kloer, D.P. / Welsch, R. / Beyer, P. / Schulz, G.E. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Structure and Reaction Geometry of Geranylgeranyl Diphosphate Synthase from Sinapis Alba. Authors: Kloer, D.P. / Welsch, R. / Beyer, P. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j1p.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j1p.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/2j1p ftp://data.pdbj.org/pub/pdb/validation_reports/j1/2j1p | HTTPS FTP |
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-Related 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 oper: (Code: given Matrix: (-0.87173, -0.20486, -0.44511), Vector: |
-Components
#1: Protein | Mass: 32134.703 Da / Num. of mol.: 2 / Fragment: RESIDUES 74-301,316-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SINAPIS ALBA (white mustard) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q43133 #2: Chemical | ChemComp-GRG / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.39 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97967 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97967 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34 Å / Num. obs: 94523 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 91.5 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 1.8→32 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.775 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.12 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→32 Å
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Refine LS restraints |
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