+Open data
-Basic information
Entry | Database: PDB / ID: 6nko | |||||||||
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Title | Crystal structure of ForH | |||||||||
Components | ForH | |||||||||
Keywords | UNKNOWN FUNCTION / Apo structure / Formycin A | |||||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase activity / purine nucleotide biosynthetic process Similarity search - Function | |||||||||
Biological species | Streptomyces kaniharaensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å | |||||||||
Authors | Zheng, J. / Irani, S. / Zhang, Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2019 Title: Identification of the Formycin A Biosynthetic Gene Cluster from Streptomyces kaniharaensis Illustrates the Interplay between Biological Pyrazolopyrimidine Formation and de Novo Purine Biosynthesis. Authors: Wang, S.A. / Ko, Y. / Zeng, J. / Geng, Y. / Ren, D. / Ogasawara, Y. / Irani, S. / Zhang, Y. / Liu, H.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nko.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nko.ent.gz | 123.9 KB | Display | PDB format |
PDBx/mmJSON format | 6nko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nko_validation.pdf.gz | 450.1 KB | Display | wwPDB validaton report |
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Full document | 6nko_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 6nko_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 6nko_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/6nko ftp://data.pdbj.org/pub/pdb/validation_reports/nk/6nko | HTTPS FTP |
-Related structure data
Related structure data | 1m9nS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 23192.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces kaniharaensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8H038*PLUS #2: 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: 2.82 Å3/Da / Density % sol: 56.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2016 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 41344 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 15.14 |
Reflection shell | Resolution: 2.4→2.44 Å / Num. unique obs: 4551 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1M9N Resolution: 2.403→48.93 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.403→48.93 Å
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Refine LS restraints |
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LS refinement shell |
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