+Open data
-Basic information
Entry | Database: PDB / ID: 3bwn | ||||||
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Title | L-tryptophan aminotransferase | ||||||
Components | (L-tryptophan ...) x 2 | ||||||
Keywords | TRANSFERASE / aminotransferase / auxin synthesis / tryptophan / pyridoxal-5'-phosphate / indole-3-pyruvate | ||||||
Function / homology | Function and homology information tryptophan transaminase / L-tryptophan-pyruvate aminotransferase / indoleacetic acid biosynthetic process / cotyledon vascular tissue pattern formation / L-phenylalanine-pyruvate transaminase activity / L-tryptophan:2-oxoglutarate aminotransferase activity / L-tryptophan:pyruvate aminotransferase activity / L-tyrosine-pyruvate transaminase activity / L-methionine:2-oxoglutarate aminotransferase activity / L-glutamine:2-oxoglutarate aminotransferase activity ...tryptophan transaminase / L-tryptophan-pyruvate aminotransferase / indoleacetic acid biosynthetic process / cotyledon vascular tissue pattern formation / L-phenylalanine-pyruvate transaminase activity / L-tryptophan:2-oxoglutarate aminotransferase activity / L-tryptophan:pyruvate aminotransferase activity / L-tyrosine-pyruvate transaminase activity / L-methionine:2-oxoglutarate aminotransferase activity / L-glutamine:2-oxoglutarate aminotransferase activity / gynoecium development / L-alanine:2-oxoglutarate aminotransferase activity / primary root development / maintenance of root meristem identity / cotyledon development / shoot system development / L-phenylalanine-2-oxoglutarate transaminase activity / shade avoidance / positive gravitropism / phloem or xylem histogenesis / carbon-sulfur lyase activity / auxin polar transport / response to ethylene / leaf development / root development / flower development / L-leucine:2-oxoglutarate aminotransferase activity / L-tyrosine-2-oxoglutarate transaminase activity / embryo development ending in seed dormancy / amino acid metabolic process / pyridoxal phosphate binding / defense response to bacterium / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 2.25 Å | ||||||
Authors | Ferrer, J.-L. / Noel, J.P. / Pojer, F. / Bowman, M. / Chory, J. / Tao, Y. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2008 Title: Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants Authors: Tao, Y. / Ferrer, J.L. / Ljung, K. / Pojer, F. / Hong, F. / Long, J.A. / Li, L. / Moreno, J.E. / Bowman, M.E. / Ivans, L.J. / Cheng, Y. / Lim, J. / Zhao, Y. / Ballare, C.L. / Sandberg, G. / ...Authors: Tao, Y. / Ferrer, J.L. / Ljung, K. / Pojer, F. / Hong, F. / Long, J.A. / Li, L. / Moreno, J.E. / Bowman, M.E. / Ivans, L.J. / Cheng, Y. / Lim, J. / Zhao, Y. / Ballare, C.L. / Sandberg, G. / Noel, J.P. / Chory, J. #1: Journal: To be Published Title: Structural basis for entry of L-TRP into pathway for auxin biosynthesis Authors: Ferrer, J.-L. / Tao, Y. / Pojer, F. / Bowman, M.E. / Chory, J. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bwn.cif.gz | 861.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bwn.ent.gz | 710.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bwn_validation.pdf.gz | 546.3 KB | Display | wwPDB validaton report |
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Full document | 3bwn_full_validation.pdf.gz | 611.4 KB | Display | |
Data in XML | 3bwn_validation.xml.gz | 90.3 KB | Display | |
Data in CIF | 3bwn_validation.cif.gz | 123 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/3bwn ftp://data.pdbj.org/pub/pdb/validation_reports/bw/3bwn | HTTPS FTP |
-Related structure data
Related structure data | 1lk9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-L-tryptophan ... , 2 types, 6 molecules ABDEFC
#1: Protein | Mass: 44864.020 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g70560/F5A18_26, F5A18.26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9S7N2 #2: Protein | | Mass: 45092.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g70560/F5A18_26, F5A18.26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9S7N2 |
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-Non-polymers , 4 types, 598 molecules
#3: Chemical | ChemComp-PMP / #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-PHE / | #6: 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: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: 13-19% PEG 3350, 0.3M KCl, 100mM MOPSO pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97944 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2006 / Details: MIRRORS + DOUBLE MONOCHROMATOR |
Radiation | Monochromator: SI (111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 110711 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.49 % / Rsym value: 0.56 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 2.41 % / Mean I/σ(I) obs: 2.53 / Rsym value: 0.414 / % possible all: 82.6 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY Starting model: PDB ENTRY 1LK9 Resolution: 2.25→29.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 19.051 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→29.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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