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Yorodumi- PDB-4rdu: Crystal structure of a distal-less homeobox protein 5 (Dlx5) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rdu | ||||||
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Title | Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PF00046 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / TRANSCRIPTION / TRANSCRIPTION-DNA complex / Partnership for Stem Cell Biology / STEMCELL | ||||||
Function / homology | Function and homology information interneuron axon guidance / olfactory pit development / HMG box domain binding / olfactory bulb interneuron differentiation / anatomical structure formation involved in morphogenesis / Specification of the neural plate border / endochondral ossification / embryonic limb morphogenesis / face morphogenesis / inner ear morphogenesis ...interneuron axon guidance / olfactory pit development / HMG box domain binding / olfactory bulb interneuron differentiation / anatomical structure formation involved in morphogenesis / Specification of the neural plate border / endochondral ossification / embryonic limb morphogenesis / face morphogenesis / inner ear morphogenesis / roof of mouth development / BMP signaling pathway / epithelial cell differentiation / positive regulation of epithelial cell proliferation / skeletal system development / osteoblast differentiation / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of canonical Wnt signaling pathway / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL) | ||||||
Citation | Journal: To be published Title: Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rdu.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rdu.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rdu_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 4rdu_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 4rdu_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 4rdu_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/4rdu ftp://data.pdbj.org/pub/pdb/validation_reports/rd/4rdu | HTTPS FTP |
-Related structure data
Related structure data | 1ig7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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-Components
#1: Protein | Mass: 7663.090 Da / Num. of mol.: 2 / Fragment: DNA binding residues 137-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BC006226, DLX5 / Plasmid: pET28bGB1Tev / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56178 #2: DNA chain | ( Mass: 4279.804 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (135-198) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (135-198) WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.28 Å3/Da / Density % sol: 46.05 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.08M sodium chloride, 45.00% 2-methyl-2,4-pentanediol, 0.012M spermine tetrahydrochloride, 0.1M sodium cacodylate pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 24, 2014 Details: Vertical focusing mirror; double crystal Si(111) monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→22.303 Å / Num. all: 23348 / Num. obs: 23348 / % possible obs: 95.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 33.646 Å2 / Rsym value: 0.046 / Net I/σ(I): 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IG7 Resolution: 1.85→22.303 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 6.492 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.TLS GROUPS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD (MOTION DETERMINATION) SERVER. 4. WATERS WERE EXCLUDED FROM TLS ASSIGNMENT.
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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 max: 158.2 Å2 / Biso mean: 47.0789 Å2 / Biso min: 20.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→22.303 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.85→1.897 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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