+Open data
-Basic information
Entry | Database: PDB / ID: 6l4b | ||||||
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Title | Crystal structure of human WT NDRG3 | ||||||
Components | Protein NDRG3 | ||||||
Keywords | SIGNALING PROTEIN / alpha/beta-hydrolase fold / NDRG3 / Unfolded helix | ||||||
Function / homology | Function and homology information negative regulation of cell growth / spermatogenesis / cell differentiation / signal transduction / extracellular exosome / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kim, K.R. / Han, B.W. | ||||||
Citation | Journal: Biomolecules / Year: 2020 Title: Structural and Biophysical Analyses of Human N-Myc Downstream-Regulated Gene 3 (NDRG3) Protein. Authors: Kim, K.R. / Kim, K.A. / Park, J.S. / Jang, J.Y. / Choi, Y. / Lee, H.H. / Lee, D.C. / Park, K.C. / Yeom, Y.I. / Kim, H.J. / Han, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l4b.cif.gz | 335.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l4b.ent.gz | 271.9 KB | Display | PDB format |
PDBx/mmJSON format | 6l4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l4b_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 6l4b_full_validation.pdf.gz | 470.2 KB | Display | |
Data in XML | 6l4b_validation.xml.gz | 57 KB | Display | |
Data in CIF | 6l4b_validation.cif.gz | 78.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/6l4b ftp://data.pdbj.org/pub/pdb/validation_reports/l4/6l4b | HTTPS FTP |
-Related structure data
Related structure data | 6l4gC 6l4hC 2xmqS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 41449.586 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NDRG3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGV2 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 200 mM sodium citrate tribasic dehydrate, 20% PEG 3350 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 23, 2018 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.2→50 Å / Num. obs: 95796 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.9 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.641 / Num. unique obs: 4774 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XMQ Resolution: 2.2→46.671 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.036 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.604 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→46.671 Å
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Refine LS restraints |
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LS refinement shell |
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