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Yorodumi- PDB-2g64: Structure of Caenorhabditis elegans 6-pyruvoyl tetrahydropterin s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g64 | ||||||
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Title | Structure of Caenorhabditis elegans 6-pyruvoyl tetrahydropterin synthase | ||||||
Components | Putative 6-pyruvoyl tetrahydrobiopterin synthase | ||||||
Keywords | LYASE / TETRAHYDROBIOPTERIN BIOSYNTHESIS / PHOSPHATE ELIMINATION / PTERINE SYNTHESIS / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / 6-pyruvoyltetrahydropterin synthase / 6-pyruvoyltetrahydropterin synthase activity / tetrahydrobiopterin biosynthetic process / mitochondrion / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wengerter, B.C. / Patskovsky, Y. / Zhan, C. / Ramagopal, U. / Milstein, S. / Vidal, M. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Caenorhabditis Elegans 6-Pyruvoyl Tetrahydropterin Synthase Authors: Wengerter, B.C. / Patskovsky, Y. / Zhan, C. / Ramagopal, U. / Milstein, S. / Vidal, M. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g64.cif.gz | 49 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g64.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 2g64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g64_validation.pdf.gz | 433 KB | Display | wwPDB validaton report |
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Full document | 2g64_full_validation.pdf.gz | 433.6 KB | Display | |
Data in XML | 2g64_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 2g64_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/2g64 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/2g64 | HTTPS FTP |
-Related structure data
Related structure data | 1b66S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16055.360 Da / Num. of mol.: 1 / Mutation: C140S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: B0041.6 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI References: UniProt: O02058, 6-pyruvoyltetrahydropterin synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-GOL / | #5: 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: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 MM HEPES, 1 M SODIUM SUCCINATE, PH 7.00, 1% PEG 2000ME, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 2006 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 14091 / Num. obs: 14091 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.031 / Rsym value: 0.03 / Net I/σ(I): 38.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 14.6 / Num. unique all: 1380 / Rsym value: 0.103 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B66 Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.541 / SU ML: 0.081 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.126 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.347 Å2
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Refine analyze | Luzzati coordinate error obs: 0.171 Å / Luzzati d res low obs: 5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 20
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