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- PDB-2bnz: Structural basis for cooperative binding of Ribbon-Helix-Helix Om... -
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Basic information
Entry | Database: PDB / ID: 2bnz | ||||||
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Title | Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats | ||||||
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![]() | DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX / RIBBON-HELIX-HELIX / RHH / METJ/ARC SUPERFAMILY / COOPERATIVE DNA BINDING / INC18 FAMILY | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weihofen, W.A. / Cicek, A. / Pratto, F. / Alonso, J.C. / Saenger, W. | ||||||
![]() | ![]() Title: Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription. Authors: Weihofen, W.A. / Cicek, A. / Pratto, F. / Alonso, J.C. / Saenger, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.1 KB | Display | ![]() |
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PDB format | ![]() | 57.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2bnwSC ![]() 2caxC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE DESIGNATION OF THE QUATERNARY STRUCTURE AS OCTAMERICREFLECTS THE STANDARD PQS CONVENTION FOR DESCRIBINGHETEROGENEOUS ASSEMBLIES. HOWEVER, THE CRYSTALLOGRAPHICASYMMETRIC UNIT ACTUALLY CONTAINS ONE DNA FRAGMENT(COMPRISED OF CHAINS E AND F) WHICH IS BOUND TO TWOPROTEIN DIMERS (CHAINS A, B, C AND D). A FURTHER FREEDNA FRAGMENT (CHAINS G AND H) IS PRESENT IN THE A.U. BUTIS LARGELY UNOBSERVED IN ELECTRON DENSITY MAPS. |
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Components
#1: Protein | Mass: 6137.223 Da / Num. of mol.: 4 / Fragment: RIBBON-HELIX-HELIX DOMAIN, RESIDUES 20-71 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: OMEGA TRANSCRIPTIONAL REPRESSOR IS ENCODED BY PLASMID PSM19035 OF THE INC18 FAMILY OF PLASMIDS Plasmid: PET28A-DELTA19OMEGA / Production host: ![]() ![]() #2: DNA chain | Mass: 5548.630 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID PSM19035 Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | Mass: 5481.564 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID PSM19035 Source: (synth.) SYNTHETIC CONSTRUCT (others) #4: Water | ChemComp-HOH / | Sequence details | 19 N-TERMINAL RESIDUES TRUNCATED, NEW N-TERMINAL MET19 IS A CLONING ARTEFACT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.9 % |
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Crystal grow | pH: 7.5 Details: 120 MM NA/KPO4, PH 7.2, 2.2 M DINATRIUMMALONATE, PH 7.5, 3 % 2-METHYL-2,4-PENTANDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→35 Å / Num. obs: 18516 / % possible obs: 92.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.1 / % possible all: 72.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BNW Resolution: 2.6→100 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.877 / SU B: 18.753 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NUCLEOTIDES G5-G16, G18, E18 AND H19-H31 WERE NOT MODELLED DUE TO PATCHY ELECTRON DENSITY
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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: 34.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→100 Å
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Refine LS restraints |
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