+Open data
-Basic information
Entry | Database: PDB / ID: 1a1k | ||||||
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Title | RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GACC SITE) | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / COMPLEX (ZINC FINGER-DNA) / ZINC FINGER / DNA-BINDING PROTEIN / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / positive regulation of gene expression via chromosomal CpG island demethylation / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / : / BMP signaling pathway / positive regulation of smooth muscle cell migration / skeletal muscle cell differentiation / locomotor rhythm / T cell differentiation / estrous cycle / RNA polymerase II core promoter sequence-specific DNA binding / long-term memory / response to glucose / regulation of neuron apoptotic process / positive regulation of chemokine production / positive regulation of smooth muscle cell proliferation / positive regulation of miRNA transcription / positive regulation of interleukin-1 beta production / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / regulation of long-term neuronal synaptic plasticity / circadian regulation of gene expression / response to insulin / negative regulation of canonical Wnt signaling pathway / cellular response to gamma radiation / positive regulation of neuron apoptotic process / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / regulation of apoptotic process / transcription cis-regulatory region binding / learning or memory / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / ISOMORPHOUS MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Elrod-Erickson, M. / Benson, T.E. / Pabo, C.O. | ||||||
Citation | Journal: Structure / Year: 1998 Title: High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Authors: Elrod-Erickson, M. / Benson, T.E. / Pabo, C.O. #1: Journal: Structure / Year: 1996 Title: Zif268 Protein-DNA Complex Refined at 1.6 A: A Model System for Understanding Zinc Finger-DNA Interactions Authors: Elrod-Erickson, M. / Rould, M.A. / Nekludova, L. / Pabo, C.O. #2: Journal: Science / Year: 1994 Title: Zinc Finger Phage: Affinity Selection of Fingers with New DNA-Binding Specificities Authors: Rebar, E.J. / Pabo, C.O. #3: Journal: Science / Year: 1991 Title: Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 A Authors: Pavletich, N.P. / Pabo, C.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a1k.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a1k.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a1k_validation.pdf.gz | 380.3 KB | Display | wwPDB validaton report |
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Full document | 1a1k_full_validation.pdf.gz | 384.2 KB | Display | |
Data in XML | 1a1k_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1a1k_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/1a1k ftp://data.pdbj.org/pub/pdb/validation_reports/a1/1a1k | HTTPS FTP |
-Related structure data
Related structure data | 1a1fC 1a1gC 1a1hC 1a1iC 1a1jC 1a1lC 1aayS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3399.223 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 3310.161 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 10795.463 Da / Num. of mol.: 1 / Fragment: ZINC FINGER Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PRADR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P08046 | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.26 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: 25% PEG 1450, 25 MM MES PH 6.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: YALE MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 23142 / % possible obs: 79.9 % / Observed criterion σ(I): -2 / Redundancy: 2.3 % / Rsym value: 0.034 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.258 / % possible all: 63.8 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 79.9 % / Redundancy: 2.3 % / Num. measured all: 10102 / Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 63.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AAY, WITHOUT WATERS AND WITHOUT SIDE CHAINS FOR RESIDUES 18 - 24 Resolution: 1.9→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 31.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.33 |