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- PDB-1ox6: TOWARDS UNDERSTANDING THE MECHANISM OF THE COMPLEX CYCLIZATION RE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ox6 | ||||||
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Title | TOWARDS UNDERSTANDING THE MECHANISM OF THE COMPLEX CYCLIZATION REACTION CATALYZED BY IMIDAZOLE GLYCEROPHOSPHATE SYNTHASE | ||||||
![]() | Imidazole glycerol phosphate synthase hisHF | ||||||
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Function / homology | ![]() imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / oxo-acid-lyase activity / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaudhuri, B.N. / Smith, J.L. | ||||||
![]() | ![]() Title: Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed by Imidazole Glycerophosphate Synthase: Crystal Structures of a Ternary Complex and the Free Enzyme Authors: Chaudhuri, B.N. / Lange, S.C. / Myers, R.S. / Davisson, V.J. / Smith, J.L. #1: ![]() Title: Substrate-Induced Changes in the Ammonia Channel for Imidazole Glycerol Phosphate Synthase Authors: Myers, R.S. / Jensen, J.R. / Deras, I.L. / Smith, J.L. / Davisson, V.J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.5 KB | Display | ![]() |
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PDB format | ![]() | 175.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ox4C ![]() 1ox5C ![]() 1jvnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8433, 0.1701, -0.5098), Vector ![]() |
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Components
#1: Protein | Mass: 61422.164 Da / Num. of mol.: 2 / Fragment: AMIDOTRANSFERASE AND CYCLASE DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HIS7 / Production host: ![]() ![]() ![]() References: UniProt: P33734, ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-POP / | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.3 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulfate, peg MME 5000, Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Chaudhuri, B.N., (2001) Structure, 9, 987. / PH range low: 7 / PH range high: 6.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Mar 28, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→100 Å / Num. all: 47205 / Num. obs: 47205 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / % possible all: 93.5 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 93.5 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1JVN Resolution: 2.4→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1517144.1 / Data cutoff low absF: 44.7 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Bsol: 29.2927 Å2 / ksol: 0.343148 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2.4 Å | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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