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Yorodumi- PDB-1m9n: CRYSTAL STRUCTURE OF THE HOMODIMERIC BIFUNCTIONAL TRANSFORMYLASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m9n | ||||||
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Title | CRYSTAL STRUCTURE OF THE HOMODIMERIC BIFUNCTIONAL TRANSFORMYLASE AND CYCLOHYDROLASE ENZYME AVIAN ATIC IN COMPLEX WITH AICAR AND XMP AT 1.93 ANGSTROMS. | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Wolan, D.W. / Greasly, S.E. / Beardsley, G.P. / Wilson, I.A. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structural Insights into the Avian AICAR Transformylase Mechanism. Authors: Wolan, D.W. / Greasly, S.E. / Beardsley, G.P. / Wilson, I.A. | ||||||
History |
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Remark 12 | OTHER REFINEMENT REMARKS Reported B value is prior to incorporation of tensors with TLSANL. Tensors ...OTHER REFINEMENT REMARKS Reported B value is prior to incorporation of tensors with TLSANL. Tensors have been added to the B value for the publication. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m9n.cif.gz | 248.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m9n.ent.gz | 195.3 KB | Display | PDB format |
PDBx/mmJSON format | 1m9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m9n_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1m9n_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1m9n_validation.xml.gz | 49.3 KB | Display | |
Data in CIF | 1m9n_validation.cif.gz | 69.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/1m9n ftp://data.pdbj.org/pub/pdb/validation_reports/m9/1m9n | 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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Details | Both monomers of the biologically significant avian ATIC homodimer are located within the asymmetric unit. |
-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: 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: 2.37 Å3/Da / Density % sol: 48.16 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 8000, imidazole, DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 1999 Details: bent conical Si-mirror (Rh coating); bent cylindrical Ge(111) monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→30 Å / Num. all: 92862 / Num. obs: 91184 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 33.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 4619 / Rsym value: 0.419 / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 99.6 % / Num. unique obs: 4619 / Rmerge(I) obs: 0.419 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G8M Resolution: 1.93→29.24 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.949 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→29.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.933→1.983 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS Lowest resolution: 29.2 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.206 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.93 Å / Lowest resolution: 1.98 Å |