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Open data
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Basic information
Entry | Database: PDB / ID: 1g2d | ||||||
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Title | STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (CLONE #2) | ||||||
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![]() | TRANSCRIPTION/DNA / phage display / zinc finger-DNA complex / TATA box / Cys2His2 / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() 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 / : / 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 / BMP signaling pathway / long-term memory / response to glucose / regulation of neuron apoptotic process / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / 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 miRNA transcription / positive regulation of neuron apoptotic process / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / sequence-specific DNA binding / learning or memory / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wolfe, S.A. / Grant, R.A. / Elrod-Erickson, M. / Pabo, C.O. | ||||||
![]() | ![]() Title: Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Authors: Wolfe, S.A. / Grant, R.A. / Elrod-Erickson, M. / Pabo, C.O. #1: ![]() Title: A General Strategy for Selecting High-Affinity Zinc Finger Proteins for Diverse DNA Target Sites Authors: Griesman, H.A. / Pabo, C.O. #2: ![]() Title: Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions Authors: Elrod-Erickson, M. / Rould, R.A. / Nekludova, L. / Pabo, C.O. #3: ![]() Title: Analysis of Zinc Fingers Optimized via Phage Display: Evaluating the Utility of a Recognition Code Authors: Wolfe, S.A. / Griesman, H.A. / Ramm, E.I. / Pabo, C.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.4 KB | Display | ![]() |
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PDB format | ![]() | 65.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 4980.269 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 4815.126 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 10713.330 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 69.2 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 400, NaCl, Bis-Tris Propane, CoCl2, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 27, 2000 / Details: Yale mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 32875 / Num. obs: 358651 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.91 % / Biso Wilson estimate: 31 Å2 / Rsym value: 6.6 / Net I/σ(I): 30.04 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 9 % / Mean I/σ(I) obs: 9.35 / Num. unique all: 3182 / Rsym value: 44.8 / % possible all: 95.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 32875 / Num. measured all: 358651 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.448 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: TATA structure of clone #6 solved by MIRAS Resolution: 2.2→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 Stereochemistry target values: Xplor parameter set: param19.sol;parhcsdx.pro;dna-rna.param
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Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor obs: 0.225 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.397 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.362 |