+Open data
-Basic information
Entry | Database: PDB / ID: 3m70 | ||||||
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Title | Crystal Structure of TehB from Haemophilus influenzae | ||||||
Components | Tellurite resistance protein tehB homolog | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / tellurite resistance / PSI-2 / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS / Cytoplasm | ||||||
Function / homology | Function and homology information response to tellurium ion / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Chen, Y.-H. / Hendrickson, W.A. / New York Consortium on Membrane Protein Structure (NYCOMPS) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of TehB from Haemophilus influenzae Authors: Chen, Y.-H. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m70.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m70.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 3m70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/3m70 ftp://data.pdbj.org/pub/pdb/validation_reports/m7/3m70 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33481.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: KW20 / Gene: HI1275, Rd, tehB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45134 |
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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: 3.19 Å3/Da / Density % sol: 61.45 % |
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Crystal grow | Temperature: 298 K / pH: 6.5 Details: 25% PEG3350,100mM Bis-Tris pH 6.5, 200mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 33498 / % possible obs: 96.6 % / Redundancy: 13.8 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 4.9 / % possible all: 74.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.876 / SU ML: 0.088 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.301 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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