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Yorodumi- PDB-2zw2: Crystal Structure of Formylglycinamide Ribonucleotide Amidotransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zw2 | ||||||
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Title | Crystal Structure of Formylglycinamide Ribonucleotide Amidotransferase III from SULFOLOBUS TOKODAII (STPURS) | ||||||
Components | Putative uncharacterized protein STS178 | ||||||
Keywords | LIGASE / Purine metabolism | ||||||
Function / homology | Function and homology information phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Suzuki, S. / Tamura, S. / Okada, K. / Baba, S. / Kumasaka, T. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / Sampei, G. / Kawai, G. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Formylglycinamide Ribonucleotide Amidotransferase III from SULFOLOBUS TOKODAII (STPURS) Authors: Suzuki, S. / Tamura, S. / Okada, K. / Baba, S. / Kumasaka, T. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / Sampei, G. / Kawai, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zw2.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zw2.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zw2_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 2zw2_full_validation.pdf.gz | 442.6 KB | Display | |
Data in XML | 2zw2_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 2zw2_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/2zw2 ftp://data.pdbj.org/pub/pdb/validation_reports/zw/2zw2 | HTTPS FTP |
-Related structure data
Related structure data | 1vq3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10763.329 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: purS / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami (DE3) References: UniProt: Q970V8, UniProt: F9VNF4*PLUS, phosphoribosylformylglycinamidine 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: 1.95 Å3/Da / Density % sol: 36.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES sodium pH7.5, 0.8M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 30, 2008 |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 24008 / Num. obs: 24008 / % possible obs: 97.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1925 / % possible all: 79.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VQ3 Resolution: 1.55→24.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 315431.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.154 Å2 / ksol: 0.408065 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→24.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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