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- PDB-2bnw: Structural basis for cooperative binding of Ribbon-Helix-Helix Om... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bnw | ||||||
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Title | Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to direct DNA heptad repeats | ||||||
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![]() | DNA-BINDING/REGULATORY PROTEIN / DNA-BINDING-REGULATORY PROTEIN COMPLEX / RIBBON-HELIX-HELIX / RHH / METJ/ARC SUPERFAMILY / COOPERATIVE DNA BINDING / INVERTED REPEATS / DNA HEPTAD / INC18 FAMILY / DNA-BINDING REGULATORY PROTEIN | ||||||
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 | ![]() | 93.5 KB | Display | ![]() |
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PDB format | ![]() | 68.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.3 KB | Display | ![]() |
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Full document | ![]() | 486.7 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bnzC ![]() 2caxC ![]() 1cmaS ![]() 1irqS 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.THE INTERFACE BETWEEN THE TWO PROTEIN DIMERS AND DNAIS 1600 ANGSTROMS**2 AND THE INTERFACE BETWEEN THETWO PROTEIN DIMERS IS 280 ANSGTROMS**2. |
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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: 5486.610 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DIRECT DNA HEPTAD REPEATS OCCUR IN PROMOTERS PRECEEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL EPRESSOR, INC18 FAMILY OF PLASMIDS Source: (synth.) synthetic construct #3: DNA chain | Mass: 5543.584 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DIRECT DNA HEPTAD REPEATS OCCUR IN PROMOTERS PRECEEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL EPRESSOR, INC18 FAMILY OF PLASMIDS Source: (synth.) synthetic construct #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: 4 Å3/Da / Density % sol: 69 % |
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Crystal grow | pH: 7 Details: 150 MM NA/KPO4, PH 7.0, 2.4 NA2MALONATE, PH 7.5, 2% AMINOCAPROIC ACID |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 28, 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: 2.45→30 Å / Num. obs: 83105 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3 / % possible all: 81.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IRQ AND 1CMA Resolution: 2.45→43.44 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.188 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CYTOSINES E18 AND G18 WERE ONLY MODELED FOR THE 5'- PHOSPATE AND ATOM C5'
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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: 45.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→43.44 Å
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Refine LS restraints |
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