+Open data
-Basic information
Entry | Database: PDB / ID: 2htm | ||||||
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Title | Crystal structure of TTHA0676 from Thermus thermophilus HB8 | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / thiamin biosynthesis / ThiG / Thermus thermophilus HB8 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information thiazole synthase / sulfurtransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Sugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of TTHA0676 from Thermus thermophilus HB8 Authors: Sugahara, M. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2htm.cif.gz | 237 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2htm.ent.gz | 190.7 KB | Display | PDB format |
PDBx/mmJSON format | 2htm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/2htm ftp://data.pdbj.org/pub/pdb/validation_reports/ht/2htm | HTTPS FTP |
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-Related structure data
Related structure data | 1wv2S 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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3 |
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Unit cell |
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Details | The biological assembly is a tetramer in the asymmetric unit. |
-Components
#1: Protein | Mass: 28482.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Tissue: HB8 / Plasmid: pET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKG7 #2: Protein | Mass: 7132.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Tissue: HB8 / Plasmid: pET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKG8, UniProt: Q72KL7*PLUS #3: 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: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7.5 Details: PEG 4000, HEPES, pH 7.5, microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97908 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 53298 / Num. obs: 53298 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 44.41 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.059 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5282 / Rsym value: 0.328 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WV2 Resolution: 2.3→19.96 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 47.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.027
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