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Yorodumi- PDB-2c3z: Crystal structure of a truncated variant of indole-3-glycerol pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c3z | ||||||
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Title | Crystal structure of a truncated variant of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus | ||||||
Components | INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE | ||||||
Keywords | LYASE / INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE / PROTEIN STABILITY / CATALYTIC ACTIVITY / DIVERGENT EVOLUTION / TRYPTOPHAN BIOSYNTHESIS / DECARBOXYLASE | ||||||
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 | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.8 Å | ||||||
Authors | Schneider, A. / Knoechel, T. / Darimont, B. / Hennig, M. / Dietrich, S. / Kirschner, K. / Sterner, R. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Role of the N-Terminal Extension of the (Betaalpha)(8)-Barrel Enzyme Indole-3-Glycerol Phosphate Synthase for its Fold, Stability, and Catalytic Activity. Authors: Schneider, B. / Knoechel, T. / Darimont, B. / Hennig, M. / Dietrich, S. / Babinger, K. / Kirschner, K. / Sterner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c3z.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c3z.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 2c3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c3z_validation.pdf.gz | 403.3 KB | Display | wwPDB validaton report |
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Full document | 2c3z_full_validation.pdf.gz | 412.2 KB | Display | |
Data in XML | 2c3z_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 2c3z_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/2c3z ftp://data.pdbj.org/pub/pdb/validation_reports/c3/2c3z | HTTPS FTP |
-Related structure data
Related structure data | 1igsS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 25476.309 Da / Num. of mol.: 1 / Fragment: DELTA(1-26), RESIDUES 27-248 Source method: isolated from a genetically manipulated source Details: N-TERMINALLY TRUNCATED FRAGMENT OF INDOLE -3-GLYCEROL PHOSPHATE SYNTHASE (RESIDUES 27-248) Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q06121, indole-3-glycerol-phosphate synthase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Compound details | INVOLVED IN AMINO-ACID BIOSYNTHES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.9 % |
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Crystal grow | Details: 30% PEG8000 0.2 M AMMONIUM SULFATE 0.1 M MES, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→12 Å / Num. obs: 5474 / % possible obs: 96.4 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1IGS Resolution: 2.8→10 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Total num. of bins used: 8 /
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