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- PDB-2dj6: Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dj6 | ||||||
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Title | Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3 | ||||||
![]() | hypothetical protein PH0634 | ||||||
![]() | LYASE / 6-pyruvoyl tetrahydrobiopterin synthase (PTPS) / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() 6-carboxy-5,6,7,8-tetrahydropterin synthase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3 Authors: Bagautdinov, B. / Kunishima, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.9 KB | Display | ![]() |
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PDB format | ![]() | 62.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.8 KB | Display | ![]() |
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Full document | ![]() | 452.5 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Trimer (A,B and C) in the assymmetric unit represents a biological unit |
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Components
#1: Protein | Mass: 13532.464 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 3257041, UniProt: O58368*PLUS, 6-pyruvoyltetrahydropterin synthase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % |
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Crystal grow | Temperature: 291 K / Method: microbathch / pH: 6.25 Details: 16.5% PEG 20000, 0.1M Acetate, NAOH pH 6.25, microbathch, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→47.85 Å / Num. all: 21576 / Num. obs: 21534 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 66.05 Å2 / Rmerge(I) obs: 0.276 / Rsym value: 0.262 / Net I/σ(I): 9.9 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.07 / Num. unique all: 2094 / Rsym value: 0.262 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 39.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→33.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.028
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