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- PDB-2xmq: Crystal structure of human NDRG2 protein provides insight into it... -
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Open data
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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 | ||||||
![]() | PROTEIN NDRG2 | ||||||
![]() | SIGNALING PROTEIN | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hwang, J. / Kim, Y. / Lee, H. / Kim, M.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173 KB | Display | ![]() |
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PDB format | ![]() | 138.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.6 KB | Display | ![]() |
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Full document | ![]() | 484 KB | Display | |
Data in XML | ![]() | 34.3 KB | Display | |
Data in CIF | ![]() | 45.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qmqSC ![]() 2xmrC ![]() 2xmsC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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