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Yorodumi- PDB-7aw9: CCAAT-binding complex and HapX bound to Aspergillus fumigatus cccA DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aw9 | |||||||||
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Title | CCAAT-binding complex and HapX bound to Aspergillus fumigatus cccA DNA | |||||||||
Components |
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Keywords | TRANSCRIPTION / transcription factor / histone fold / basic leucine zipper / heteropentamer / protein-DNA complex | |||||||||
Function / homology | Function and homology information negative regulation of iron ion transport / : / CCAAT-binding factor complex / regulation of carbohydrate metabolic process / RNA polymerase II transcription regulator complex / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / intracellular iron ion homeostasis / sequence-specific DNA binding / transcription cis-regulatory region binding ...negative regulation of iron ion transport / : / CCAAT-binding factor complex / regulation of carbohydrate metabolic process / RNA polymerase II transcription regulator complex / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / intracellular iron ion homeostasis / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Aspergillus nidulans FGSC A4 (mold) Emericella nidulans (mold) Aspergillus fumigatus A1163 (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Huber, E.M. / Groll, M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Structure / Year: 2022 Title: Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX. Authors: Huber, E.M. / Hortschansky, P. / Scheven, M.T. / Misslinger, M. / Haas, H. / Brakhage, A.A. / Groll, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aw9.cif.gz | 273.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aw9.ent.gz | 218.4 KB | Display | PDB format |
PDBx/mmJSON format | 7aw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/7aw9 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/7aw9 | HTTPS FTP |
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-Related structure data
Related structure data | 7aw7SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 7669.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ANIA_07545 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EAZ0 |
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#2: Protein | Mass: 10641.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ANIA_04034 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5B5Z6 |
#3: Protein | Mass: 13666.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: AN6492.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5AYY8 |
#4: Protein | Mass: 11479.957 Da / Num. of mol.: 2 / Mutation: C92K, C129S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold) Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ANIA_08251 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EAX9 |
-DNA chain , 2 types, 2 molecules FG
#5: DNA chain | Mass: 11507.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus fumigatus A1163 (mold) |
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#6: DNA chain | Mass: 11263.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus fumigatus A1163 (mold) |
-Non-polymers , 1 types, 1 molecules
#7: Chemical | ChemComp-CL / |
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-Details
Has ligand of interest | N |
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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: 3.14 Å3/Da / Density % sol: 60.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH 8.5, 25 % PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→47 Å / Num. obs: 12478 / % possible obs: 97.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 988 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AW7 Resolution: 3.5→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 101.093 / SU ML: 0.645 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.68 / 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: 316.22 Å2 / Biso mean: 172.965 Å2 / Biso min: 106.46 Å2
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Refinement step | Cycle: final / Resolution: 3.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.59 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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