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Yorodumi- PDB-4opl: Constructing tailored isoprenoid products by structure-guided mod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4opl | ||||||
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Title | Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase. | ||||||
Components | Conserved Archaeal protein | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Archaeal Protein | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-CH group of donors / glycerophospholipid metabolic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / phospholipid biosynthetic process Similarity search - Function | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | McAndrew, R.P. / Kung, Y. / Xie, X. / Liu, C. / Pereira, J.H. / Keasling, J.D. / Adams, P.D. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase. Authors: Kung, Y. / McAndrew, R.P. / Xie, X. / Liu, C.C. / Pereira, J.H. / Adams, P.D. / Keasling, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4opl.cif.gz | 190.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4opl.ent.gz | 160.5 KB | Display | PDB format |
PDBx/mmJSON format | 4opl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4opl_validation.pdf.gz | 708.8 KB | Display | wwPDB validaton report |
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Full document | 4opl_full_validation.pdf.gz | 714.5 KB | Display | |
Data in XML | 4opl_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4opl_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/4opl ftp://data.pdbj.org/pub/pdb/validation_reports/op/4opl | HTTPS FTP |
-Related structure data
Related structure data | 4opcC 4opdC 4opgC 4opiC 4optC 4opuC 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: 50862.027 Da / Num. of mol.: 1 / Mutation: I206F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 Gene: Saci_0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JA33, EC: 1.3.1.83 |
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#2: Chemical | ChemComp-FDA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Tris pH 7.5, 10% PEG 3350 and 0.2 M L-proline, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2012 |
Radiation | Monochromator: Double crystal Si(111)and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→50 Å / Num. all: 20447 / Num. obs: 19915 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % |
Reflection shell | Resolution: 2.48→2.52 Å / Redundancy: 5.7 % / % possible all: 77.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→43.984 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 32.08 / 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: 2.51→43.984 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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