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Yorodumi- PDB-3d7j: SCO6650, a 6-pyruvoyltetrahydropterin synthase homolog from Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d7j | ||||||
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Title | SCO6650, a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor | ||||||
Components | Uncharacterized protein SCO6650 | ||||||
Keywords | UNKNOWN FUNCTION / T-fold | ||||||
Function / homology | Function and homology information 6-carboxytetrahydropterin synthase / 6-carboxy-5,6,7,8-tetrahydropterin synthase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å | ||||||
Authors | Spoonamore, J.E. / Roberts, S.A. / Heroux, A. / Bandarian, V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Structure of a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor. Authors: Spoonamore, J.E. / Roberts, S.A. / Heroux, A. / Bandarian, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d7j.cif.gz | 176 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d7j.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 3d7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d7j_validation.pdf.gz | 473.7 KB | Display | wwPDB validaton report |
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Full document | 3d7j_full_validation.pdf.gz | 478 KB | Display | |
Data in XML | 3d7j_validation.xml.gz | 37 KB | Display | |
Data in CIF | 3d7j_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/3d7j ftp://data.pdbj.org/pub/pdb/validation_reports/d7/3d7j | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16684.355 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A(3)2 / Gene: SCO6650 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O86696 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2 M NaCl, 10% PEG6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-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: 1.45→41.34 Å / Num. all: 141171 / Num. obs: 140447 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 44 | ||||||||||||||||||
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7012 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.45→41.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.313 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGEN ATOMS HAVE BEEN ADDED IN 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: 20.396 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→41.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.485 Å / Total num. of bins used: 20
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