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Yorodumi- PDB-4b2g: Crystal Structure of an Indole-3-Acetic Acid Amido Synthase from ... -
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-Basic information
Entry | Database: PDB / ID: 4b2g | ||||||
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Title | Crystal Structure of an Indole-3-Acetic Acid Amido Synthase from Vitis vinifera Involved in Auxin Homeostasis | ||||||
Components | GH3-1 AUXIN CONJUGATING ENZYME | ||||||
Keywords | SIGNALING PROTEIN / IGNALING PROTEIN / ADENYLATE / AMINO ACID CONJUGATION / PLANT GROWTH | ||||||
Function / homology | GH3 family / GH3 auxin-responsive promoter / acid-amino acid ligase activity / cytoplasm / MALONATE ION / Chem-V1N / Uncharacterized protein Function and homology information | ||||||
Biological species | VITIS VINIFERA (wine grape) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Peat, T.S. / Bottcher, C. / Newman, J. / Lucent, D. / Cowieson, N. / Davies, C. | ||||||
Citation | Journal: Plant Cell / Year: 2012 Title: Crystal Structure of an Indole-3-Acetic Acid Amido Synthetase from Grapevine Involved in Auxin Homeostasis. Authors: Peat, T.S. / Bottcher, C. / Newman, J. / Lucent, D. / Cowieson, N. / Davies, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b2g.cif.gz | 238.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b2g.ent.gz | 192.5 KB | Display | PDB format |
PDBx/mmJSON format | 4b2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/4b2g ftp://data.pdbj.org/pub/pdb/validation_reports/b2/4b2g | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 68681.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VITIS VINIFERA (wine grape) / Strain: CABERNET SAUVIGNON / Description: CABERNET SAUVIGNON FROM SOUTH AUSTRALIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: F6H697 #2: Chemical | ChemComp-MLI / #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | MALONATE ION (MLI): USED AS A CRYSTALLIZ | Sequence details | LAST 11 RESIDUES ARE PART OF A HIS-TAG ADDED TO THE PROTEIN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.5 % Description: STRUCTURE WAS SOLVED INITIALLY WTH A SINGLE PT DERIVATIVE AND LATER REFINED TO HIGHER RESOLUTION, 2.40 A, USING A SECOND NATIVE DATA SET. |
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Crystal grow | Temperature: 293 K / pH: 7 Details: THE PROTEIN WAS CONCENTRATED TO 6 MG/ML IN THE PRESENCE OF 10 MM INHIBITOR AND CRYSTALLIZED AT 20 DEGREES CELSIUS IN 0.7 TO 1.0 M SODIUM MALONATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→338.07 Å / Num. obs: 59192 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 14.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.37→2.5 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.794 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE NOT MODELLED UNLESS THERE WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE NOT MODELLED UNLESS THERE WAS SUFFICIENT DENSITY FOR AT LEAST THE BACKBONE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.482 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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