+Open data
-Basic information
Entry | Database: PDB / ID: 1b66 | ||||||
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Title | 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE | ||||||
Components | 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE | ||||||
Keywords | TETRAHYDROBIOPTERIN BIOSYNTHESIS / PHOSPHATE ELIMINATION / PTERINE SYNTHESIS | ||||||
Function / homology | Function and homology information Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / 6-pyruvoyltetrahydropterin synthase / 6-pyruvoyltetrahydropterin synthase activity / 6-carboxy-5,6,7,8-tetrahydropterin synthase activity / tetrahydrobiopterin biosynthetic process / mitochondrion / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Rattus rattus (black rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ploom, T. / Thoeny, B. / Yim, J. / Lee, S. / Nar, H. / Leimbacher, W. / Huber, R. / Richardson, J. / Auerbach, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystallographic and kinetic investigations on the mechanism of 6-pyruvoyl tetrahydropterin synthase. Authors: Ploom, T. / Thony, B. / Yim, J. / Lee, S. / Nar, H. / Leimbacher, W. / Richardson, J. / Huber, R. / Auerbach, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b66.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b66.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 1b66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b66_validation.pdf.gz | 390.5 KB | Display | wwPDB validaton report |
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Full document | 1b66_full_validation.pdf.gz | 394.4 KB | Display | |
Data in XML | 1b66_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1b66_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/1b66 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/1b66 | HTTPS FTP |
-Related structure data
Related structure data | 1b6zC 1gtqS S: Starting model for refinement 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.383926, 0.923363, -0.001366), Vector: |
-Components
#1: Protein | Mass: 15875.165 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / Organ: LIVER / Production host: Escherichia coli (E. coli) / References: UniProt: P27213, EC: 4.6.1.10 #2: Chemical | #3: Chemical | #4: 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: 4.03 Å3/Da / Density % sol: 69.45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.2 / Details: pH 9.2 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 40302 / % possible obs: 99.5 % / Observed criterion σ(I): 1.7 / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 |
Reflection | *PLUS Lowest resolution: 28 Å / Num. measured all: 156350 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 97.7 % / Rmerge(I) obs: 0.413 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GTQ Resolution: 1.9→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1.7
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Displacement parameters | Biso mean: 22.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev Biso : 1.14 Å2 / Rms dev position: 0.16 Å / Weight Biso : 1 / Weight position: 25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Rfactor Rfree: 0.338 / Rfactor obs: 0.329 |