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Yorodumi- PDB-2ip4: Crystal Structure of Glycinamide Ribonucleotide Synthetase from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ip4 | ||||||
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Title | Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8 | ||||||
Components | Phosphoribosylamine--glycine ligase | ||||||
Keywords | LIGASE / GAR synthetase / PurD / thermus thermophilus / purine nucleotide / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / purine nucleobase biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Sampei, G. / Baba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / Kawai, H. / Fukai, Y. / Ebihara, A. / Nakagawa, N. / Kawai, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biochem. / Year: 2010 Title: Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria Authors: Sampei, G. / Baba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / Kawai, H. / Fukai, Y. / Ebihara, A. / Nakagawa, N. / Kawai, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ip4.cif.gz | 164.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ip4.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ip4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ip4_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 2ip4_full_validation.pdf.gz | 491.3 KB | Display | |
Data in XML | 2ip4_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 2ip4_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/2ip4 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/2ip4 | HTTPS FTP |
-Related structure data
Related structure data | 2yrwC 2yrxC 2ys6C 2ys7C 2yw2C 2yyaC 1gsoS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44888.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0811 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q5SK40, phosphoribosylamine-glycine ligase #2: Chemical | ChemComp-SO4 / #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: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M ammonium sulfate, 0.1M MES, 30% PEGMME5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9843 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 6, 2004 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9843 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→60 Å / Num. all: 30609 / Num. obs: 29262 / % possible obs: 95.6 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GSO Resolution: 2.8→60 Å / Cross valid method: FREE R / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→60 Å
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