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Yorodumi- PDB-3tc6: Crystal Structure of Engineered Protein. Northeast Structural Gen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tc6 | ||||||
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Title | Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR63. | ||||||
Components | Indole-3-glycerol phosphate synthase | ||||||
Keywords | LYASE / Structural Genomics / Engineered Protein / Northeast Structural Genomics Consortium / NESG / OR63 / PSI-Biology | ||||||
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 P2 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Vorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Baker, D. ...Vorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design. Authors: Bjelic, S. / Kipnis, Y. / Wang, L. / Pianowski, Z. / Vorobiev, S. / Su, M. / Seetharaman, J. / Xiao, R. / Kornhaber, G. / Hunt, J.F. / Tong, L. / Hilvert, D. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tc6.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tc6.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 3tc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/3tc6 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/3tc6 | HTTPS FTP |
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-Related structure data
Related structure data | 3tc7C 1julS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | monomer,30.47 kD,97.1% |
-Components
#1: Protein | Mass: 29653.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: trpC, SSO0895 / Production host: Escherichia coli (E. coli) References: UniProt: Q06121, indole-3-glycerol-phosphate synthase | ||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 277 K / Method: microbatch crystallization under oil / pH: 5 Details: 40% PEG 400, 0.1 M Sodium phosphate monobasic, 0.1 M Sodium acetate, pH 5.0, Microbatch crystallization under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 10, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 129900 / Num. obs: 129900 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.06 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.19 / Num. unique all: 12870 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1jul Resolution: 1.6→31.633 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.93 / Phase error: 17.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.764 Å2 / ksol: 0.407 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.03 Å2 / Biso mean: 19.468 Å2 / Biso min: 2.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→31.633 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24 / % reflection obs: 100 %
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