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Yorodumi- PDB-2xmq: Crystal structure of human NDRG2 protein provides insight into it... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xmq | ||||||
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Title | Crystal structure of human NDRG2 protein provides insight into its role as a tumor suppressor | ||||||
Components | PROTEIN NDRG2 | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / vascular associated smooth muscle cell proliferation / negative regulation of cytokine production / negative regulation of vascular associated smooth muscle cell proliferation / substantia nigra development / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / growth cone / cell differentiation ...regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / vascular associated smooth muscle cell proliferation / negative regulation of cytokine production / negative regulation of vascular associated smooth muscle cell proliferation / substantia nigra development / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / growth cone / cell differentiation / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Hwang, J. / Kim, Y. / Lee, H. / Kim, M.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal Structure of Human Ndrg2 Protein Provides Insight Into its Role as a Tumor Suppressor. Authors: Hwang, J. / Kim, Y. / Kang, H.B. / Jaroszewski, L. / Deacon, A. / Lee, H. / Choi, W.C. / Kim, K.J. / Kim, C.H. / Kang, B.S. / Lee, J.O. / Oh, T.K. / Kim, J.W. / Wilson, I.A. / Kim, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xmq.cif.gz | 173 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xmq.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/2xmq ftp://data.pdbj.org/pub/pdb/validation_reports/xm/2xmq | HTTPS FTP |
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-Related structure data
Related structure data | 2qmqSC 2xmrC 2xmsC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 24 - 304 / Label seq-ID: 1 - 281
NCS ensembles :
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-Components
#1: Protein | Mass: 31338.482 Da / Num. of mol.: 3 / Fragment: ALPHA-BETA HYDROLASE DOMAIN, RESIDUES 24-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9UN36 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | Details: 9% PEG 8000, 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE (PH 6.4 TO 7.5). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9795 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→40 Å / Num. obs: 24361 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.5 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QMQ Resolution: 2.81→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.885 / SU B: 15.182 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.372 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→40 Å
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Refine LS restraints |
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