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Yorodumi- PDB-2w7n: Crystal Structure of KorA Bound to Operator DNA: Insight into Rep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w7n | ||||||
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Title | Crystal Structure of KorA Bound to Operator DNA: Insight into Repressor Cooperation in RP4 Gene Regulation | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / INCP / PLASMID / REPRESSOR / DNA-BINDING / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / HELIX-TURN-HELIX MOTIF / TRANSCRIPTION REGULATION / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Koenig, B. / Mueller, J.J. / Lanka, E. / Heinemann, U. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2009 Title: Crystal Structure of Kora Bound to Operator DNA: Insight Into Repressor Cooperation in Rp4 Gene Regulation Authors: Koenig, B. / Mueller, J.J. / Lanka, E. / Heinemann, U. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w7n.cif.gz | 167.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w7n.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 2w7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/2w7n ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w7n | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.2408, 0.1716, 0.9553), Vector: |
-Components
#1: Protein | Mass: 11323.908 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PMS51-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03052 #2: DNA chain | Mass: 5547.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) #3: DNA chain | Mass: 5675.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) #4: 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: 3.6 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.5M (NH4)2SO4, 0.1M C6H5NA3O7 2H2O (PH 5.6), 1.0M LI2SO4 H2O, VAPOR DIFFUSION, HANGING DROP, 291 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91991 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 27, 2006 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91991 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 31085 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 42.5 |
Reflection shell | Resolution: 1.96→2.08 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 17.4 / % possible all: 70.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.85→57.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.935 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.125 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→57.74 Å
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Refine LS restraints |
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