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Yorodumi- PDB-2czg: Crystal structure of Probable phosphoribosylglycinamide formyl tr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2czg | ||||||
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Title | Crystal structure of Probable phosphoribosylglycinamide formyl transferase (PH0318) from Pyrococcus horikoshii OT3 | ||||||
Components | phosphoribosylglycinamide formyl transferase | ||||||
Keywords | TRANSFERASE / Purine ribonucleotide biosynthesis / phosphoribosylglycinamide formyltransferase / PurT / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information phosphoribosylglycinamide formyltransferase 2 / phosphoribosylglycinamide formyltransferase 2 activity / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / ligase activity / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Yoshikawa, S. / Arai, R. / Kamo-Uchikubo, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Probable phosphoribosylglycinamide formyl transferase (PH0318) from Pyrococcus horikoshii OT3 Authors: Yoshikawa, S. / Arai, R. / Kamo-Uchikubo, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2czg.cif.gz | 175.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2czg.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 2czg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2czg_validation.pdf.gz | 473.9 KB | Display | wwPDB validaton report |
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Full document | 2czg_full_validation.pdf.gz | 497.8 KB | Display | |
Data in XML | 2czg_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 2czg_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/2czg ftp://data.pdbj.org/pub/pdb/validation_reports/cz/2czg | HTTPS FTP |
-Related structure data
Related structure data | 1kjiS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48774.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0318 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CodonPlus-RIL References: GenBank: 14590236, UniProt: O58056*PLUS, Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: 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: 3.58 Å3/Da / Density % sol: 65.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.5M Ammonium Sulfate, 25% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: May 26, 2005 / Details: two dimensional focusing mirror |
Radiation | Monochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 57729 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.92 % / Biso Wilson estimate: 27.2 Å2 / Rsym value: 0.074 / Net I/σ(I): 19.35 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 5 % / Mean I/σ(I) obs: 5.57 / Num. unique all: 5750 / Rsym value: 0.263 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1kji Resolution: 2.35→49.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3536064.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.5983 Å2 / ksol: 0.38513 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→49.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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