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Yorodumi- PDB-2ywc: Crystal structure of GMP synthetase from Thermus thermophilus in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ywc | ||||||
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Title | Crystal structure of GMP synthetase from Thermus thermophilus in complex with XMP | ||||||
Components | GMP synthase [glutamine-hydrolyzing] | ||||||
Keywords | LIGASE / GMP synthetase / XMP binding / ATP binding / Purine nucleotide biosynthetic pathway / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information GMP synthase activity / GMP synthase (glutamine-hydrolysing) / glutamine metabolic process / ATP binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Baba, S. / Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. / Sampei, G. / Kawai, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of GMP synthetase from Thermus thermophilus Authors: Baba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / Kuramitsu, S. / Yokoyama, 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 | 2ywc.cif.gz | 378.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ywc.ent.gz | 309.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ywc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ywc_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2ywc_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2ywc_validation.xml.gz | 75.5 KB | Display | |
Data in CIF | 2ywc_validation.cif.gz | 101.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/2ywc ftp://data.pdbj.org/pub/pdb/validation_reports/yw/2ywc | HTTPS FTP |
-Related structure data
Related structure data | 2ywbSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 56128.621 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: guaA / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) References: UniProt: Q5SI28, GMP synthase (glutamine-hydrolysing) #2: Chemical | ChemComp-XMP / #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: 2.91 Å3/Da / Density % sol: 57.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: 1.2M NaCl, 0.1M Sodium Acetate, 10mM XMP, pH4.4, 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: 0.97891 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 17, 2006 |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 126620 / % possible obs: 98.3 % / Redundancy: 5.5 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.799 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YWB Resolution: 2.2→31.82 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 102105.82 / 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: 52.4081 Å2 / ksol: 0.349749 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→31.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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