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Yorodumi- PDB-2b1g: Crystal structures of transition state analogue inhibitors of ino... -
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-Basic information
Entry | Database: PDB / ID: 2b1g | ||||||
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Title | Crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase | ||||||
Components | Bifunctional purine biosynthesis protein PURH | ||||||
Keywords | TRANSFERASE / HYDROLASE / ATIC / IMPCH / structure-base / transition state analogue / inhibitor | ||||||
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: 2.1 Å | ||||||
Authors | Xu, L. / Chong, Y. / Hwang, I. / D'Onofrio, A. / Amore, K. / Beardsley, G.P. / Li, C. / Olson, A.J. / Boger, D.L. / Wilson, I.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structure-based Design, Synthesis, Evaluation, and Crystal Structures of Transition State Analogue Inhibitors of Inosine Monophosphate Cyclohydrolase. Authors: Xu, L. / Chong, Y. / Hwang, I. / D'Onofrio, A. / Amore, K. / Beardsley, G.P. / Li, C. / Olson, A.J. / Boger, D.L. / Wilson, I.A. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structure of avian AICAR transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening Authors: Xu, L. / Li, C. / Olson, A.J. / Wilson, I.A. #2: Journal: J.Med.Chem. / Year: 2004 Title: Successful virtual screening for human AICAR transformylase inhibitors against NCI diversity set using AutoDock. Authors: Li, C. / Xu, L. / Wolan, D.W. / Wilson, I.A. / Olson, A.J. #3: Journal: Nat.Struct.Mol.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. #4: Journal: Biochemistry / Year: 2002 Title: Structural insights into the avian AICAR transformylase mechanism Authors: Wolan, D.W. / Greasley, S.E. / Beardsley, G.P. / Wilson, I.A. #5: 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. #6: Journal: Biochemistry / Year: 2004 Title: Structural insights into the human and avian IMP cyclohydrolase mechanism via crystal structures with the bound XMP Inhibitor Authors: Wolan, D.W. / Cheong, C.-G. / Greasley, S.E. / Wilson, I.A. #7: Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structures of human bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase/IMP cyclohydrolase in complex with potent sulfonyl-containing antifolates Authors: Cheong, C.G. / Wolan, D.W. / Greasley, S.E. / Horton, P.A. / Beardsley, G.P. / 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 | 2b1g.cif.gz | 894 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b1g.ent.gz | 746.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/2b1g ftp://data.pdbj.org/pub/pdb/validation_reports/b1/2b1g | HTTPS FTP |
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-Related structure data
Related structure data | 2b1iC 2iu0C 2iu3C 1g8mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A, B, C &D) |
-Components
#1: Protein | Mass: 64497.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Includes Phosphoribosylaminoimidazolecarboxamide formyltransferase (AICAR transformylase), IMP cyclohydrolase (Inosinicase, IMP synthetase, ATIC) Source: (gene. exp.) Gallus gallus (chicken) / Gene: ATIC, PURH / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P31335, IMP cyclohydrolase, phosphoribosylaminoimidazolecarboxamide formyltransferase #2: Chemical | #3: Chemical | ChemComp-K / #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: 2.6 Å3/Da / Density % sol: 52.8 % |
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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 |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1271 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Apr 7, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 131382 / Rmerge(I) obs: 0.06 / Χ2: 1.361 / D res high: 2.1 Å / D res low: 50 Å / % possible obs: 83.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.1→50 Å / Num. all: 131382 / Num. obs: 118497 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 38.2 Å2 / Rsym value: 0.06 / Χ2: 1.361 / Net I/σ(I): 11.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.14 Å / % possible obs: 42.2 % / Redundancy: 1.2 % / Mean I/σ(I) obs: 1.3 / Num. measured obs: 3334 / Num. unique all: 3334 / Rsym value: 0.351 / Χ2: 0.59 / % possible all: 42.2 |
-Phasing
Phasing MR | Rfactor: 46.9 / Cor.coef. Fo:Fc: 36.8
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G8M Resolution: 2.1→41.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.13 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.215 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.044 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→41.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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