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Yorodumi- PDB-2iu3: Crystal structures of transition state analogue inhibitors of ino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iu3 | ||||||
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Title | Crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase | ||||||
Components | BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH | ||||||
Keywords | HYDROLASE / MULTIFUNCTIONAL ENZYME / TRANSITION STATE ANALOGUE / ATIC / IMPCH / INHIBITOR / TRANSFERASE / STRUCTURE-BASE / PURINE BIOSYNTHESIS | ||||||
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: 2.9 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. / Olson, A.J. / Wilson, I.A. #3: 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. #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 | 2iu3.cif.gz | 233.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iu3.ent.gz | 186.6 KB | Display | PDB format |
PDBx/mmJSON format | 2iu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/2iu3 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/2iu3 | HTTPS FTP |
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-Related structure data
Related structure data | 2b1gC 2b1iC 2iu0C 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8023, -0.1781, 0.5697), Vector: |
-Components
#1: Protein | Mass: 64497.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: BIFUNCTIONAL ENZYME / Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P31335, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase #2: Chemical | #3: Chemical | ChemComp-203 / | #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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | pH: 7.2 Details: 20%PEG8000, 0.2 M IMIDAZOLE PH7.2, 5MM DTT, 0.01M HEXAMINECOBALT TRICHLORIDE, pH 7.20 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 14, 2006 / Details: MIRROR |
Radiation | Monochromator: SIDE SCATTERING BENT CUBE- ROOT-BEAM SINGLE CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 30321 / % possible obs: 98 % / Observed criterion σ(I): 4 / Redundancy: 3.1 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.5 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G8M Resolution: 2.9→35.2 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 91596.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: MAXIUM LIKELIHOOD
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Solvent computation | Solvent model: BULK SOLVENT CORRECTION / Bsol: 22.34 Å2 / ksol: 0.279 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→35.2 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAIN | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: YC103.PAR / Topol file: YC103.TOP |