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Yorodumi- PDB-5jfq: Geranylgeranyl Pyrophosphate Synthetase from archaeon Geoglobus a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jfq | ||||||
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Title | Geranylgeranyl Pyrophosphate Synthetase from archaeon Geoglobus acetivorans | ||||||
Components | Geranylgeranyl Pyrophosphate Synthetase | ||||||
Keywords | OXIDOREDUCTASE / Geranylgeranyl Pyrophosphate Synthetase / hyperthermophilic / archaeon | ||||||
Function / homology | Function and homology information geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyltranstransferase activity / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Geoglobus acetivorans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Petrova, T. / Boyko, K.M. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Rakitin, A.L. / Ravin, N.V. / Popov, V.O. | ||||||
Citation | Journal: Extremophiles / Year: 2018 Title: Structural characterization of geranylgeranyl pyrophosphate synthase GACE1337 from the hyperthermophilic archaeon Geoglobus acetivorans. Authors: Petrova, T.E. / Boyko, K.M. / Nikolaeva, A.Y. / Stekhanova, T.N. / Gruzdev, E.V. / Mardanov, A.V. / Stroilov, V.S. / Littlechild, J.A. / Popov, V.O. / Bezsudnova, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jfq.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jfq.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jfq_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 5jfq_full_validation.pdf.gz | 441.4 KB | Display | |
Data in XML | 5jfq_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 5jfq_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/5jfq ftp://data.pdbj.org/pub/pdb/validation_reports/jf/5jfq | HTTPS FTP |
-Related structure data
Related structure data | 1wy0S 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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Unit cell |
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-Components
#1: Protein | Mass: 36250.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Protein: AIY90378 / Source: (gene. exp.) Geoglobus acetivorans (archaea) / Gene: GACE_1337 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): DLT1270 / References: UniProt: A0A0A7GEY4 #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: 2.41 Å3/Da / Density % sol: 48.97 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Tris pH 8.0, 0.1M sodium malonate pH 8.0, 33% PEG 1000 and 10% ethylene glycol mixed with protein in ratio 1:1 over 500 ml of precipitant solution covered with oils |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→94.08 Å / Num. obs: 24891 / % possible obs: 99.8 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.309 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.51→2.62 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WY0 Resolution: 2.51→78.112 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.27 / Phase error: 29 / 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→78.112 Å
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Refine LS restraints |
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LS refinement shell |
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