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- PDB-5app: Actinobacillus actinomycetemcomitans OMP100 residues 133-198 fuse... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5app | ||||||
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Title | Actinobacillus actinomycetemcomitans OMP100 residues 133-198 fused to GCN4 adaptors | ||||||
![]() | General control protein GCN4,GENERAL CONTROL PROTEIN GCN4, OUTER MEMBRANE PROTEIN 100,General control protein GCN4 | ||||||
![]() | MEMBRANE PROTEIN / FUSION PROTEIN / ALPHA/BETA COILED COIL / BETA LAYER / TRIMER / CHIMERA | ||||||
Function / homology | ![]() protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hartmann, M.D. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
![]() | ![]() Title: alpha / beta coiled coils. Authors: Hartmann, M.D. / Mendler, C.T. / Bassler, J. / Karamichali, I. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.7 KB | Display | ![]() |
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PDB format | ![]() | 125.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 449.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5apqC ![]() 5apsC ![]() 5aptC ![]() 5apuC ![]() 5apvC ![]() 5apwC ![]() 5apxC ![]() 5apyC ![]() 5apzC ![]() 2wpqS C: citing same article ( S: Starting model for refinement |
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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 domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 15441.728 Da / Num. of mol.: 3 Fragment: UNP RESIDUES P03069 250-277, G4B386 133-199, P03069 250-277,UNP RESIDUES P03069 250-277, G4B386 133-199, P03069 250-277,UNP RESIDUES P03069 250-277, G4B386 133-199, P03069 250-277 Mutation: YES,YES,YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GCN4, AAS3, ARG9, YEL009C / Production host: ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | Details: 0.1 M TRI-SODIUM CITRATE PH 5.5, 2 %(V/V) DIOXANE 15 %(W/V) PEG 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 27, 2008 | ||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→32.9 Å / Num. obs: 18247 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 2.84 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14 | ||||||||||||||||||||
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.88 / % possible all: 86.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WPQ Resolution: 2.3→32.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.99 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.347 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→32.9 Å
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Refine LS restraints |
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