[English] 日本語
Yorodumi- PDB-1uth: DntR from Burkholderia sp. strain DNT in complex with Thiocyanate -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uth | ||||||
---|---|---|---|---|---|---|---|
Title | DntR from Burkholderia sp. strain DNT in complex with Thiocyanate | ||||||
Components | (LYSR-TYPE REGULATORY PROTEIN) x 2 | ||||||
Keywords | TRANSCRIPTION REGULATION / LYSR / TRANSCRIPTIONAL REGULATOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BURKHOLDERIA SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Smirnova, I.A. / Dian, C. / Leonard, G.A. / McSweeney, S. / Birse, D. / Brzezinski, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Development of a Bacterial Biosensor for Nitrotoluenes: The Crystal Structure of the Transcriptional Regulator Dntr Authors: Smirnova, I.A. / Dian, C. / Leonard, G.A. / Mcsweeney, S. / Birse, D. / Brzezinski, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1uth.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1uth.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 1uth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uth_validation.pdf.gz | 458.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1uth_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 1uth_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1uth_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/1uth ftp://data.pdbj.org/pub/pdb/validation_reports/ut/1uth | HTTPS FTP |
-Related structure data
Related structure data | 1utbSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.5951, -0.7802, 0.1925), Vector: |
-Components
#1: Protein | Mass: 35544.973 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA SP. (bacteria) / Strain: DNT / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7WT50 | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 35489.891 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA SP. (bacteria) / Strain: DNT / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7WT50 | ||||||
#3: Chemical | ChemComp-SCN / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | THE SEQUENCE CRYSTALLISED DIFFERS FROM Q7WT50 IN THAT IT CONTAINS A T192S MUTATION, AN ADDITIONAL 8 ...THE SEQUENCE CRYSTALLIS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.9 % |
---|---|
Crystal grow | pH: 8.5 / Details: pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.932 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 50319 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UTB Resolution: 2.2→95.35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.325 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME ATOMS IN A NUMBER OF SIDE CHAINS HAVE BEEN ASSIGNED OCCUPANCIES OF LESS THAN ONE. THIS PROBABLY REFLECTS RADIATION DAMAGE TO THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME ATOMS IN A NUMBER OF SIDE CHAINS HAVE BEEN ASSIGNED OCCUPANCIES OF LESS THAN ONE. THIS PROBABLY REFLECTS RADIATION DAMAGE TO THE CRYSTAL. ADDITIONALLY, A NUMBER OF SIDE CHAINS HAVE BEEN TRUNCATED TO REFLECT THE APPEARANCE OF THE ELECTRON DENSITY FOR THESE RESIDUES
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 41.67 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→95.35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|