+Open data
-Basic information
Entry | Database: PDB / ID: 5ndy | ||||||
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Title | crystal structure of variants | ||||||
Components | Geranylgeranylglyceryl phosphate synthase | ||||||
Keywords | TRANSFERASE / Methanobacterium thermoautotrophicum | ||||||
Function / homology | Function and homology information phosphoglycerol geranylgeranyltransferase / phosphoglycerol geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / polyprenyltransferase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus str. Delta H (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å | ||||||
Authors | Linde, M. / Rajendran, C. / Babinger, P. / Sterner, R. | ||||||
Citation | Journal: To Be Published Title: crystal structure of variants from MtGGGPS Authors: Sterner, R. / Babinger, P. / Linde, M. / Rajendran, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ndy.cif.gz | 275.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ndy.ent.gz | 233.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ndy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5ndy ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5ndy | 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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-Components
#1: Protein | Mass: 27679.436 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea) Gene: MTH_552 / Production host: Escherichia coli (E. coli) References: UniProt: O26652, phosphoglycerol geranylgeranyltransferase #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: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: PEG, Tris Cl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.949→49.773 Å / Num. obs: 125165 / % possible obs: 97.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.06882 / Rpim(I) all: 0.0283 / Rrim(I) all: 0.07452 / Net I/σ(I): 17.16 |
Reflection shell | Rmerge(I) obs: 1.068 / Rpim(I) all: 1.16 / Rrim(I) all: 0.4461 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.949→49.773 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.949→49.773 Å
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Refine LS restraints |
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LS refinement shell |
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