+Open data
-Basic information
Entry | Database: PDB / ID: 2yqy | ||||||
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Title | Crystal structure of TT2238, a four-helix bundle protein | ||||||
Components | Hypothetical protein TTHA0303 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / four-helix-bundle / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | DinB-like domain / DinB superfamily / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / DinB_2 domain-containing protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Nagata, K. / Ohtsuka, J. / Iino, H. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / Tanokura, M. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 A Authors: Nagata, K. / Ohtsuka, J. / Takahashi, M. / Asano, A. / Iino, H. / Ebihara, A. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yqy.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yqy.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yqy_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 2yqy_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 2yqy_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 2yqy_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/2yqy ftp://data.pdbj.org/pub/pdb/validation_reports/yq/2yqy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18739.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a-TT2238 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q5SLJ0 #2: Water | ChemComp-HOH / | |
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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: 1.88 Å3/Da / Density % sol: 34.49 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7 Details: 20%(w/v) PEG 1000, 100mM Tris pH 7.0, 0.2M Zn acetate, microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97914, 0.97950, 0.90000 | ||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 16, 2005 Details: A fixed exit Si double crystal monochromator followed by a two dimensional focu sing mirror which is coated in rhodium. | ||||||||||||
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→36 Å / Num. all: 19790 / Num. obs: 19771 / % possible obs: 99.6 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.4 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 8.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→7.98 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.182 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.172 / 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: 20.225 Å2
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Refinement step | Cycle: LAST / Resolution: 2→7.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.048 Å / Total num. of bins used: 20
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