+Open data
-Basic information
Entry | Database: PDB / ID: 2fv2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Analysis of human Rcd-1 conserved region | ||||||
Components | RCD1 required for cell differentiation1 homolog | ||||||
Keywords | TRANSCRIPTION / ARMADILLO-REPEAT | ||||||
Function / homology | Function and homology information CCR4-NOT core complex / CCR4-NOT complex / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of epidermal growth factor receptor signaling pathway ...CCR4-NOT core complex / CCR4-NOT complex / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / nuclear receptor coactivator activity / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / positive regulation of peptidyl-serine phosphorylation / negative regulation of translation / protein domain specific binding / protein homodimerization activity / protein-containing complex / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Garces, R.G. / Gillon, W. / Pai, E.F. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties. Authors: Garces, R.G. / Gillon, W. / Pai, E.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2fv2.cif.gz | 229.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2fv2.ent.gz | 185.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/2fv2 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/2fv2 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | Biological assembly appears to be a homodimer. 2 dimers are found per asymmetric unit. |
-Components
#1: Protein | Mass: 30521.500 Da / Num. of mol.: 4 / Fragment: (Residues: 18 - 285) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Rcd1 / Plasmid: pET 32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus / References: GenBank: 4885579, UniProt: Q92600*PLUS #2: Chemical | ChemComp-MN / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.14 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 100 mM MES pH5.7, 115 mM MnSO4, 17% PEG 3350, 1% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9568, 0.9795, 0.9797, 0.9407 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2005 | |||||||||||||||
Radiation | Monochromator: Si (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. all: 152086 / Num. obs: 53307 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.033 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 89.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.2→27.26 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 550645.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.2372 Å2 / ksol: 0.346933 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.6 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→27.26 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|