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Yorodumi- PDB-1oz0: CRYSTAL STRUCTURE OF THE HOMODIMERIC BIFUNCTIONAL TRANSFORMYLASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oz0 | ||||||
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Title | CRYSTAL STRUCTURE OF THE HOMODIMERIC BIFUNCTIONAL TRANSFORMYLASE AND CYCLOHYDROLASE ENZYME AVIAN ATIC IN COMPLEX WITH A MULTISUBSTRATE ADDUCT INHIBITOR BETA-DADF. | ||||||
Components | Bifunctional purine biosynthesis protein PURH | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wolan, D.W. / Greasley, S.E. / Wall, M.J. / Benkovic, S.J. / Wilson, I.A. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Structure of Avian AICAR Transformylase with a Multisubstrate Adduct Inhibitor beta-DADF Identifies the Folate Binding Site. Authors: Wolan, D.W. / Greasley, S.E. / Wall, M.J. / 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 | 1oz0.cif.gz | 244.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oz0.ent.gz | 195.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oz0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1oz0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1oz0_validation.xml.gz | 53.9 KB | Display | |
Data in CIF | 1oz0_validation.cif.gz | 73.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/1oz0 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/1oz0 | HTTPS FTP |
-Related structure data
Related structure data | 1g8mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Details | The asymmetric unit contains the biologically active homodimer. |
-Components
#1: Protein | Mass: 66669.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: ATIC OR PURH / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P31335, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.3 Å3/Da / Density % sol: 45.46 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 13% (w/v) PEG 8000, 0.2M imidazole, pH 7.0 and 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 29, 1998 Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 39623 / Num. obs: 39623 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 36.4 Å2 / Rsym value: 0.055 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1825 / Rsym value: 0.424 / % possible all: 85.8 |
Reflection | *PLUS Highest resolution: 2.5 Å / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 85.8 % / Num. unique obs: 1825 / Rmerge(I) obs: 0.424 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G8M Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 46.89 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.5→2.52 Å / Total num. of bins used: 50
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |