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Yorodumi- PDB-1wkc: Crystal structure of a 5-formyltetrahydrofolate cycloligase-relat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wkc | ||||||
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Title | Crystal structure of a 5-formyltetrahydrofolate cycloligase-related protein from Thermus thermophilus HB8 | ||||||
Components | HB8 TT1367 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HB8 / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information 5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Yanai, H. / Tsuge, H. / Utsunomiya, H. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a 5-formyltetrahydrofolate cycloligase-related protein from Thermus thermophilus HB8 Authors: Yanai, H. / Tsuge, H. / Utsunomiya, H. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wkc.cif.gz | 46 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wkc.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 1wkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wkc_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 1wkc_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 1wkc_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1wkc_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/1wkc ftp://data.pdbj.org/pub/pdb/validation_reports/wk/1wkc | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20457.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: B834(DE3) / Production host: Escherichia coli (E. coli) / References: GenBank: 55981580, UniProt: Q5SHW9*PLUS | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 2.7 Å3/Da / Density % sol: 53.3 % |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97923, 0.97954, 0.90000 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 20, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→60.86 Å / Num. obs: 23751 / % possible obs: 99.6 % / Redundancy: 7.04 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.7 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 7.13 % / Rmerge(I) obs: 0.264 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→19.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 1.972 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.702 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20 /
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