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Yorodumi- PDB-3cin: CRYSTAL STRUCTURE OF A MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cin | |||||||||
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Title | CRYSTAL STRUCTURE OF A MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED PROTEIN (TM_1419) FROM THERMOTOGA MARITIMA MSB8 AT 1.70 A RESOLUTION | |||||||||
Components | Myo-inositol-1-phosphate synthase-related protein | |||||||||
Keywords | ISOMERASE / MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | |||||||||
Function / homology | Function and homology information inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: To be published Title: Crystal structure of MYO-inositol-1-phosphate synthase-related protein (TM1419) from Thermotoga maritima at 1.70 A resolution Authors: Joint Center for Structural Genomics (JCSG) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cin.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cin.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 3cin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/3cin ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3cin | 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 | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 43705.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM1419, TM_1419 / Plasmid: MH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9X1D6, inositol-3-phosphate synthase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-NAD / | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: NANODROP, 0.2M MgCl2, 40.0% PEG 400, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2003 / Details: KOHZU: Double Crystal Si(111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→41.135 Å / Num. obs: 43592 / % possible obs: 93.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.939 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.172 / Net I/σ(I): 21.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GR0 Resolution: 1.7→41.135 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.19 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. RESIDUE ASP 208 IS A RAMACHANDRAN OUTLIER, HOWEVER, THE ELECTRON DENSITY IS UNAMBIGUOUS FOR THIS RESIDUE. 3. CHLORINE ATOMS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. RESIDUE ASP 208 IS A RAMACHANDRAN OUTLIER, HOWEVER, THE ELECTRON DENSITY IS UNAMBIGUOUS FOR THIS RESIDUE. 3. CHLORINE ATOMS WERE MODELED SINCE THEY REFINED TO A BETTER B-FACTOR AGREEMENT WITH SURROUNDING RESIDUES. 4. THE NICOTINAMIDE RING WAS MODELED IN THE SAME ORIENTATION AS OBSERVED IN HOMOLOGS, DESPITE RESIDUAL FO-FC DENSITY INDICATION AT LEAST PARTIAL OCCUPANCY OF THE ORIENTATION ROTATED BY 180 DEGREES. 5. MAGNESIUM WAS MODELED BASED ON COORDINATION GEOMETRY AND ELECTRON DENSITY PEAK HEIGHT. 6. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.035 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→41.135 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.747 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.2655 Å / Origin y: 18.7264 Å / Origin z: 40.872 Å
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