+Open data
-Basic information
Entry | Database: PDB / ID: 6k96 | ||||||
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Title | Crystal structure of Ari2 | ||||||
Components | Five-membered-cyclitol-phosphate synthase | ||||||
Keywords | OXIDOREDUCTASE / NAD binding / Rossmann fold | ||||||
Function / homology | Function and homology information inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces citricolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Miyanaga, A. / Tsunoda, T. / Kudo, F. / Eguchi, T. | ||||||
Citation | Journal: Biochemistry / Year: 2019 Title: Stereochemistry in the Reaction of themyo-Inositol Phosphate Synthase Ortholog Ari2 during Aristeromycin Biosynthesis. Authors: Kudo, F. / Tsunoda, T. / Yamaguchi, K. / Miyanaga, A. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k96.cif.gz | 277.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k96.ent.gz | 225.5 KB | Display | PDB format |
PDBx/mmJSON format | 6k96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/6k96 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/6k96 | HTTPS FTP |
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-Related structure data
Related structure data | 1gr0S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 3 - 354 / Label seq-ID: 3 - 354
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-Components
#1: Protein | Mass: 40208.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces citricolor (bacteria) / Gene: ari2 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B4ZC85 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.58 Å3/Da / Density % sol: 65.64 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris-HCl, sodium chloride, sodium citrate, NAD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2014 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 40934 / % possible obs: 97.4 % / Redundancy: 8.4 % / Biso Wilson estimate: 38.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.138 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 5751 / CC1/2: 0.867 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GR0 Resolution: 2.5→47.18 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.872 / SU B: 23.556 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.32 Å2 / Biso mean: 42.74 Å2 / Biso min: 18.49 Å2
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Refinement step | Cycle: final / Resolution: 2.5→47.18 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9618 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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