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Yorodumi- PDB-3qn9: Crystal structure of a 6-pyruvoyltetrahydropterin synthase homolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qn9 | ||||||
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Title | Crystal structure of a 6-pyruvoyltetrahydropterin synthase homologue from Esherichia coli | ||||||
Components | 6-pyruvoyl tetrahydrobiopterin synthase | ||||||
Keywords | LYASE / 6-pyruvoyltetrahydropterin synthase / Bh4 synthase / Zn | ||||||
Function / homology | Function and homology information 6-carboxytetrahydropterin synthase / 6-carboxy-5,6,7,8-tetrahydropterin synthase activity / Lyases / queuosine biosynthetic process / zinc ion binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å | ||||||
Authors | Seo, K.H. / Zhuang, N.N. / Lee, K.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural basis of a novel activity of bacterial 6-pyruvoyltetrahydropterin synthase homologues distinct from mammalian 6-pyruvoyltetrahydropterin synthase activity. Authors: Seo, K.H. / Zhuang, N. / Park, Y.S. / Park, K.H. / Lee, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qn9.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qn9.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 3qn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qn9_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 3qn9_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 3qn9_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 3qn9_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/3qn9 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/3qn9 | HTTPS FTP |
-Related structure data
Related structure data | 3qn0C 3qnaC 2obaS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 15964.247 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Gene: EcDH1_0923 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C6EJA7, UniProt: P65870*PLUS, 6-pyruvoyltetrahydropterin synthase #2: Chemical | #3: 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: 3.94 Å3/Da / Density % sol: 68.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.02M MgCl2, 0.1M HEPES pH7.5, Polyacryslic acid 5100 sodium salt, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.123 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 13, 2007 |
Radiation | Monochromator: BRUKER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.123 Å / Relative weight: 1 |
Reflection | Resolution: 2.924→97.5 Å / Num. all: 10571 / Num. obs: 10571 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.231 |
Reflection shell | Resolution: 2.294→48.752 Å / Redundancy: 4.9 % / Num. unique all: 10571 / Rsym value: 0.231 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OBA Resolution: 2.93→48.752 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.9 / SU B: 31.351 / SU ML: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.348 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.966 Å2
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Refinement step | Cycle: LAST / Resolution: 2.93→48.752 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 934 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.928→3.004 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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