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Yorodumi- PDB-1vco: Crystal Structure of T.th. HB8 CTP synthetase complex with Glutamine -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vco | ||||||
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Title | Crystal Structure of T.th. HB8 CTP synthetase complex with Glutamine | ||||||
Components | CTP synthetase | ||||||
Keywords | LIGASE / tetramer / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / glutaminase activity / glutamine metabolic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Goto, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Structure / Year: 2004 Title: Crystal Structures of CTP Synthetase Reveal ATP, UTP, and Glutamine Binding Sites Authors: Goto, M. / Omi, R. / Nakagawa, N. / Miyahara, I. / Hirotsu, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vco.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vco.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 1vco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/1vco ftp://data.pdbj.org/pub/pdb/validation_reports/vc/1vco | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | CTPs is in an equilibrium state between a monomer, a dimer, and a tetramer depending on a protein concentration. |
-Components
#1: Protein | Mass: 61100.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5SIA8, CTP synthase (glutamine hydrolysing) |
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#2: Chemical | ChemComp-GLN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 59.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Na citrate, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 3, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.7 Å / Num. all: 40817 / Num. obs: 40404 / % possible obs: 99 % |
Reflection shell | Resolution: 2.15→2.23 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→10 Å / σ(F): 0
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→10 Å
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Refine LS restraints |
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