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Yorodumi- PDB-1i4n: CRYSTAL STRUCTURE OF INDOLEGLYCEROL PHOSPHATE SYNTHASE FROM THERM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i4n | ||||||
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Title | CRYSTAL STRUCTURE OF INDOLEGLYCEROL PHOSPHATE SYNTHASE FROM THERMOTOGA MARITIMA | ||||||
Components | INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE | ||||||
Keywords | LYASE / Indoleglycerol phosphate synthase / Thermotoga maritima / Thermostable TIM-barrel protein / Salt bridges / Electrostatic interactions | ||||||
Function / homology | Function and homology information indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Knoechel, T. / Pappenberger, A. / Jansonius, J.N. / Kirschner, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: The crystal structure of indoleglycerol-phosphate synthase from Thermotoga maritima. Kinetic stabilization by salt bridges. Authors: Knochel, T. / Pappenberger, A. / Jansonius, J.N. / Kirschner, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i4n.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i4n.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/1i4n ftp://data.pdbj.org/pub/pdb/validation_reports/i4/1i4n | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28571.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q56319, indole-3-glycerol-phosphate synthase #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: 2.6 Å3/Da / Density % sol: 52.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 8000, ammonium phosphate, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8722 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8722 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→30 Å / Num. all: 20875 / Num. obs: 20875 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.47→2.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3.6 / % possible all: 96.2 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 96.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.169 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |