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Yorodumi- PDB-2w6r: Crystal structure of an artificial (ba)8-barrel protein designed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w6r | ||||||
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Title | Crystal structure of an artificial (ba)8-barrel protein designed from identical half barrels | ||||||
Components | IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISF | ||||||
Keywords | LYASE / FUSION PROTEIN / COBALAMIN / PRECORRIN / NOVEL FOLD / VITAMIN B12 | ||||||
Function / homology | Function and homology information imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hocker, B. / Lochner, A. / Seitz, T. / Claren, J. / Sterner, R. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: High-Resolution Crystal Structure of an Artificial (Betaalpha)(8)-Barrel Protein Designed from Identical Half-Barrels. Authors: Hocker, B. / Lochner, A. / Seitz, T. / Claren, J. / Sterner, R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w6r.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w6r.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/2w6r ftp://data.pdbj.org/pub/pdb/validation_reports/w6/2w6r | HTTPS FTP |
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-Related structure data
Related structure data | 1thfS 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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-Components
#1: Protein | Mass: 29611.168 Da / Num. of mol.: 1 / Fragment: RESIDUES 123-245 AND 123-253 Source method: isolated from a genetically manipulated source Details: TWO FUSED COPIES OF THE C-TERMINAL HALF OF HISF (RESIDUE 123-253) Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET24A-HISF-CPPPC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases |
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#2: 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: 2.37 Å3/Da / Density % sol: 42.74 % / Description: RESIDUE 123-253 |
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Crystal grow | pH: 8 / Details: 0.1 M TRIS-HCL PH 8.0, 12% W/V PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 15628 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.4 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1THF Resolution: 2.1→32.95 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.632 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.209 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→32.95 Å
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Refine LS restraints |
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