+Open data
-Basic information
Entry | Database: PDB / ID: 2vuu | ||||||
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Title | Crystal structure of NADP-bound NmrA-AreA zinc finger complex | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION / PROTEIN-PROTEIN INTERACTIONS / METAL-BINDING / NITRATE ASSIMILATION / ZINC-FINGER / DNA-BINDING / ZINC FINGERS / ZINC / AREA / NMRA / NUCLEUS / ACTIVATOR / GATA-TYPE | ||||||
Function / homology | Function and homology information nitrogen catabolite repression of transcription from RNA polymerase II promoter / regulation of amide catabolic process / nitrogen catabolite repression of transcription / regulation of arginine metabolic process / regulation of nitrogen utilization / NADP+ binding / NAD+ binding / nitrate assimilation / NAD binding / regulation of gene expression ...nitrogen catabolite repression of transcription from RNA polymerase II promoter / regulation of amide catabolic process / nitrogen catabolite repression of transcription / regulation of arginine metabolic process / regulation of nitrogen utilization / NADP+ binding / NAD+ binding / nitrate assimilation / NAD binding / regulation of gene expression / sequence-specific DNA binding / oxidoreductase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | EMERICELLA NIDULANS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kotaka, M. / Johnson, C. / Lamb, H.K. / Hawkins, A.R. / Ren, J. / Stammers, D.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural Analysis of the Recognition of the Negative Regulator Nmra and DNA by the Zinc Finger from the Gata-Type Transcription Factor Area. Authors: Kotaka, M. / Johnson, C. / Lamb, H.K. / Hawkins, A.R. / Ren, J. / Stammers, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vuu.cif.gz | 581.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vuu.ent.gz | 483.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vuu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/2vuu ftp://data.pdbj.org/pub/pdb/validation_reports/vu/2vuu | HTTPS FTP |
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-Related structure data
Related structure data | 2vusC 2vutC 1k6jS 4gatS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 38835.238 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) EMERICELLA NIDULANS (mold) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O59919, UniProt: Q5AU62*PLUS #2: Protein/peptide | Mass: 4789.604 Da / Num. of mol.: 8 / Fragment: ZINC FINGER DOMAIN, RESIDUES 670-712 Source method: isolated from a genetically manipulated source Source: (gene. exp.) EMERICELLA NIDULANS (mold) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P17429 #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-ZN / #5: 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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 6.4 Details: 0.2M LI2SO4, 0.1M BIS-TRIS PH 6.4, 15% - 17% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9797 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 110086 / % possible obs: 100 % / Observed criterion σ(I): -1 / Redundancy: 8.4 % / Biso Wilson estimate: 68.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1K6J AND 4GAT Resolution: 2.8→29.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1728075.11 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: BULK SOLVENT MODEL USED A SELF PATTERSON FUNCTION SHOWED A SIGNIFICANT PEAK INDICATIVE OF PSEUDO-TRANSLATION
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.5412 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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