+Open data
-Basic information
Entry | Database: PDB / ID: 3nyz | ||||||
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Title | Crystal Structure of Kemp Elimination Catalyst 1A53-2 | ||||||
Components | Indole-3-glycerol phosphate synthase | ||||||
Keywords | LYASE / Tim Barrel / Kemp Elimination Enzyme | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.514 Å | ||||||
Authors | Lee, T.M. / Privett, H.K. / Kaiser, J.T. / Mayo, S.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Iterative approach to computational enzyme design. Authors: Privett, H.K. / Kiss, G. / Lee, T.M. / Blomberg, R. / Chica, R.A. / Thomas, L.M. / Hilvert, D. / Houk, K.N. / Mayo, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nyz.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nyz.ent.gz | 90.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/3nyz ftp://data.pdbj.org/pub/pdb/validation_reports/ny/3nyz | HTTPS FTP |
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-Related 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: 30010.518 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC / Production host: Escherichia coli (E. coli) References: UniProt: Q06121, 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: 1.86 Å3/Da / Density % sol: 33.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 bis-tris, 0.2 M ammonium acetate, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.013 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 23, 2009 / Details: Flat mirror |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.013 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→37.98 Å / Num. obs: 67105 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.51→1.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.514→36.73 Å / σ(F): 0.04 / Phase error: 27.77 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.192 Å2 / ksol: 0.394 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.514→36.73 Å
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Refine LS restraints |
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LS refinement shell |
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