[English] 日本語
Yorodumi- PDB-2dfy: Crystal structure of a cyclized protein fusion of LMO4 LIM domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dfy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a cyclized protein fusion of LMO4 LIM domains 1 and 2 with the LIM interacting domain of LDB1 | ||||||
Components | fusion protein of LIM domain transcription factor LMO4 and LIM domain-binding protein 1 | ||||||
Keywords | TRANSCRIPTION / ZINC finger / LIM only protein / LIM domain / circular protein | ||||||
Function / homology | Function and homology information regulation of cell activation / ventral spinal cord interneuron differentiation / spinal cord motor neuron cell fate specification / spinal cord association neuron differentiation / spinal cord motor neuron differentiation / regulation of cell fate specification / positive regulation of kinase activity / motor neuron axon guidance / ventricular septum development / cell leading edge ...regulation of cell activation / ventral spinal cord interneuron differentiation / spinal cord motor neuron cell fate specification / spinal cord association neuron differentiation / spinal cord motor neuron differentiation / regulation of cell fate specification / positive regulation of kinase activity / motor neuron axon guidance / ventricular septum development / cell leading edge / negative regulation of protein-containing complex assembly / regulation of cell migration / thymus development / neural tube closure / transcription corepressor activity / RNA polymerase II transcription regulator complex / DNA-binding transcription factor binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Jeffries, C.M.J. / Graham, S.C. / Collyer, C.A. / Guss, J.M. / Matthews, J.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Stabilization of a binary protein complex by intein-mediated cyclization Authors: Jeffries, C.M.J. / Graham, S.C. / Stokes, P.H. / Collyer, C.A. / Guss, J.M. / Matthews, J.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dfy.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dfy.ent.gz | 113.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/2dfy ftp://data.pdbj.org/pub/pdb/validation_reports/df/2dfy | HTTPS FTP |
---|
-Related structure data
Related structure data | 1rutS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 3 / Auth seq-ID: 19 - 327 / Label seq-ID: 2 - 174
| ||||||||||||||||||
Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT THAT CONSISTS OF 2 CHAINS. BIOLOGICAL ASSEMBLY CONSISTS OF ONE PROTEIN CHAIN, ONE HALF OF THE ASYMETRIC UNIT. |
-Components
#1: Protein | Mass: 21059.574 Da / Num. of mol.: 2 / Fragment: LMO4 / Mutation: C52S/C64S Source method: isolated from a genetically manipulated source Details: Cyclised fusion of LMO4 residues 18-152 to LDB1 LID residues 300-339 via two flexible linkers with sequence GGSGGSGGSGG and TRESGSIEF Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PNW1120, PCY76 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RECA / References: UniProt: P61969 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.7 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1M AMMONIUM SULPHATE, 0.1M TRIS, 15% GLYCEROL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2005 / Details: OSMIC 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: 1.65→50 Å / Num. all: 46870 / Num. obs: 44295 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RUT WITH MULTIPLE CONFORMERS, SOLVENT AND ZINC ATOMS REMOVED Resolution: 1.65→10 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.97 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.98 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→10 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: C / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20
|