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Yorodumi- PDB-1g8m: CRYSTAL STRUCTURE OF AVIAN ATIC, A BIFUNCTIONAL TRANSFORMYLASE AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g8m | ||||||
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Title | CRYSTAL STRUCTURE OF AVIAN ATIC, A BIFUNCTIONAL TRANSFORMYLASE AND CYCLOHYDROLASE ENZYME IN PURINE BIOSYNTHESIS AT 1.75 ANG. RESOLUTION | ||||||
Components | AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE | ||||||
Keywords | transferase / hydrolase / Homodimer / 2 functional domains / IMPCH domain = alpha/beta/alpha / AICAR Tfase = 2 alpha/beta/alpha domains / 1 alpha + beta domain | ||||||
Function / homology | Function and homology information De novo synthesis of IMP / phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Greasley, S.E. / Horton, P. / Beardsley, G.P. / Benkovic, S.J. / Wilson, I.A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis. Authors: Greasley, S.E. / Horton, P. / Ramcharan, J. / Beardsley, G.P. / Benkovic, S.J. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g8m.cif.gz | 246.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g8m.ent.gz | 204.2 KB | Display | PDB format |
PDBx/mmJSON format | 1g8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g8m_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
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Full document | 1g8m_full_validation.pdf.gz | 467.2 KB | Display | |
Data in XML | 1g8m_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 1g8m_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/1g8m ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g8m | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64966.656 Da / Num. of mol.: 2 Fragment: AMINOIMIDAZOLE CARBOXAMIDE RIBONUCLEOTIDE TRANSFORMYLASE - INOSINE MONOPHOSPHATE CYCLOHYDROLASE Mutation: MET REPLACED BY SE-MET (MSE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: PURH / Plasmid: PET 28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: P31335, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase #2: Chemical | #3: Chemical | ChemComp-G / | #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: 2.61 Å3/Da / Density % sol: 52.92 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 8000, imidazole-HCl and DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP at 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9799 / Wavelength: 0.9799, 0.9801, 0.9648 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 1999 | ||||||||||||
Radiation | Monochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→50 Å / Num. all: 229603 / Num. obs: 229603 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.8 | ||||||||||||
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.4 / % possible all: 47.3 | ||||||||||||
Reflection | *PLUS Num. measured all: 460370 | ||||||||||||
Reflection shell | *PLUS % possible obs: 47.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1962794.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.74 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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