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Yorodumi- PDB-7o9v: hypothetical protein OMM_04225 residues 244-274 from Candidatus M... -
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-Basic information
Entry | Database: PDB / ID: 7o9v | ||||||
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Title | hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors | ||||||
Components | General control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4 | ||||||
Keywords | PROTEIN FIBRIL / Coiled Coil / beta layer / hexad repeat | ||||||
Function / homology | Function and homology information 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 / sequence-specific DNA binding / transcription regulator complex / 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 | Saccharomyces cerevisiae (brewer's yeast) Candidatus Magnetoglobus multicellularis str. Araruama (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Adlakha, J. / Albrecht, R. / Hartmann, M.D. | ||||||
Citation | Journal: To Be Published Title: hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors Authors: Adlakha, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o9v.cif.gz | 115.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o9v.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 7o9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o9v_validation.pdf.gz | 448.3 KB | Display | wwPDB validaton report |
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Full document | 7o9v_full_validation.pdf.gz | 454.9 KB | Display | |
Data in XML | 7o9v_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 7o9v_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/7o9v ftp://data.pdbj.org/pub/pdb/validation_reports/o9/7o9v | HTTPS FTP |
-Related structure data
Related structure data | 2ynyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 10819.589 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Candidatus Magnetoglobus multicellularis str. Araruama (bacteria) Strain: ATCC 204508 / S288c / Gene: GCN4, AAS101, AAS3, ARG9, YEL009C, OMM_04225 / Production host: Escherichia coli (E. coli) / References: UniProt: P03069, UniProt: A0A1V1P2N3 #2: 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: 1.88 Å3/Da / Density % sol: 34.69 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2M KSCN, 0.1M bis tris propane pH 8.5, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→37.04 Å / Num. obs: 11390 / % possible obs: 89.3 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.99→2.12 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.671 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 570 / CC1/2: 0.657 / % possible all: 81.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YNY Resolution: 1.99→37.04 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.884 / SU B: 19.611 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.322 / 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 max: 111.27 Å2 / Biso mean: 44.231 Å2 / Biso min: 15.33 Å2
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Refinement step | Cycle: final / Resolution: 1.99→37.04 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.99→2.041 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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