+Open data
-Basic information
Entry | Database: PDB / ID: 2yyb | ||||||
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Title | Crystal structure of TTHA1606 from Thermus thermophilus HB8 | ||||||
Components | Hypothetical protein TTHA1606 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thermus thermophilus / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / NIF3 (NGG1p interacting factor 3)-like / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tomoike, F. / Nakagwa, N. / Ebihara, A. / Yokoyama, S. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Crystal structure of the conserved hypothetical protein TTHA1606 from Thermus thermophilus HB8. Authors: Tomoike, F. / Wakamatsu, T. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yyb.cif.gz | 104 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yyb.ent.gz | 81.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yyb_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
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Full document | 2yyb_full_validation.pdf.gz | 452.4 KB | Display | |
Data in XML | 2yyb_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 2yyb_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yyb ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yyb | HTTPS FTP |
-Related structure data
Related structure data | 1nmpS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26866.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: ttha1606 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHX4 #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: 3.86 Å3/Da / Density % sol: 68.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 28v/w PEG 400, 0.2M CaCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 11, 2007 |
Radiation | Monochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→42.78 Å / Num. all: 25740 / Num. obs: 25740 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 53.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 6.03 / Num. unique all: 2556 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NMP Resolution: 2.6→42.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 143672.6 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.1198 Å2 / ksol: 0.364834 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→42.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02
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