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Yorodumi- PDB-1eep: 2.4 A RESOLUTION CRYSTAL STRUCTURE OF BORRELIA BURGDORFERI INOSIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eep | ||||||
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Title | 2.4 A RESOLUTION CRYSTAL STRUCTURE OF BORRELIA BURGDORFERI INOSINE 5'-MONPHOSPHATE DEHYDROGENASE IN COMPLEX WITH A SULFATE ION | ||||||
Components | INOSINE 5'-MONOPHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / ALPHA-BETA BARREL / TIM BARREL / IMPDH / IMP DEHYDROGENASE / LOOP-6 / PURINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | McMillan, F.M. / Cahoon, M. / White, A. / Hedstrom, L. / Petsko, G.A. / Ringe, D. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structure at 2.4 A resolution of Borrelia burgdorferi inosine 5'-monophosphate dehydrogenase: evidence of a substrate-induced hinged-lid motion by loop 6. Authors: McMillan, F.M. / Cahoon, M. / White, A. / Hedstrom, L. / Petsko, G.A. / Ringe, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eep.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eep.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 1eep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/1eep ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1eep | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is a homo-tetramer which is generated by four monomers about a planar four fold axis. |
-Components
#1: Protein | Mass: 43827.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Production host: Escherichia coli (E. coli) / References: UniProt: P49058, IMP dehydrogenase #2: Chemical | #3: 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: 2.82 Å3/Da / Density % sol: 56.37 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein Solution: 0.16 mM protein, 0.5 M KCl, 50 mM Tris Cl (pH 7.5), 1 mM DTT, 10% glycerol, 1 mM IMP Well Solution: 2.2 M ammonium sulfate, PEG 550 MME, 0.1 M Tris Cl (pH 7.5), 10% ...Details: Protein Solution: 0.16 mM protein, 0.5 M KCl, 50 mM Tris Cl (pH 7.5), 1 mM DTT, 10% glycerol, 1 mM IMP Well Solution: 2.2 M ammonium sulfate, PEG 550 MME, 0.1 M Tris Cl (pH 7.5), 10% glycerol, 0.01 mM beta-mercaptoethanol IMP does not bind in crystal due to excess ammonium sulfate. Crystallization is reproducible in the absence of IMP. , VAPOR DIFFUSION, HANGING DROP, temperature 25K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X12B / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 11, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. all: 255126 / Num. obs: 36820 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.343 / Num. unique all: 3620 / % possible all: 95.8 |
Reflection | *PLUS Num. measured all: 255126 |
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Resolution: 2.4→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2907055.3 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 72.48 Å2 / ksol: 0.48 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.329 / % reflection Rfree: 10 % / Rfactor Rwork: 0.274 |