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Yorodumi- PDB-2qmq: Crystal structure of a n-myc downstream regulated 2 protein (ndrg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qmq | ||||||
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Title | Crystal structure of a n-myc downstream regulated 2 protein (ndrg2, syld, ndr2, ai182517, au040374) from mus musculus at 1.70 A resolution | ||||||
Components | Protein NDRG2 | ||||||
Keywords | SIGNALING PROTEIN / Alpha/beta-hydrolases fold / ndr family / developmental protein / differentiation / neurogenesis / phosphorylation / regulatory protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / postsynapse organization / negative regulation of cytokine production / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / nervous system development / growth cone / cell differentiation ...regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / postsynapse organization / negative regulation of cytokine production / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / nervous system development / growth cone / cell differentiation / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structure of the human N-Myc downstream-regulated gene 2 protein provides insight into its role as a tumor suppressor. Authors: Hwang, J. / Kim, Y. / Kang, H.B. / Jaroszewski, L. / Deacon, A.M. / 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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Remark 300 | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. | ||||||
Remark 999 | SEQUENCE THE CONSTRUCT CONSISTS OF RESIDUES 40-313 OF THE FULL LENGTH PROTEIN. IT WAS EXPRESSED ... SEQUENCE THE CONSTRUCT CONSISTS OF RESIDUES 40-313 OF THE FULL LENGTH PROTEIN. IT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qmq.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qmq.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qmq_validation.pdf.gz | 691.7 KB | Display | wwPDB validaton report |
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Full document | 2qmq_full_validation.pdf.gz | 692.4 KB | Display | |
Data in XML | 2qmq_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 2qmq_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qmq ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qmq | HTTPS FTP |
-Related structure data
Related structure data | 2xmqC 2xmrC 2xmsC 1u2eS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 32010.188 Da / Num. of mol.: 1 / Fragment: Residues 40-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: 15277975, Ndrg2, Kiaa1248, Ndr2 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9QYG0 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-BEZ / | #4: Chemical | ChemComp-2PE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.93 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: NANODROP, 20.0% PEG 400, 0.2M MgCl2, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.019976 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2005 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.019976 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.348 Å / Num. obs: 28650 / % possible obs: 92.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.405 / % possible all: 61.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U2E Resolution: 1.7→29.348 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.438 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. MG AND PEG 400 (2PE) ARE PRESENT IN THE CRYSTALLIZATION CONDITIONS. 4. THE BENZOIC ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. MG AND PEG 400 (2PE) ARE PRESENT IN THE CRYSTALLIZATION CONDITIONS. 4. THE BENZOIC ACID (BEZ) MOLECULE IS ASSIGNED BASED ON THE ELECTRON DENSITY AND ITS INTERACTION WITH THE PROTEIN. IT COULD BE SOME RELATED COMPOUND WITH A SIMILAR STRUCTURE.
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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 mean: 14.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.348 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 3.7832 Å / Origin y: 34.5458 Å / Origin z: 16.8449 Å
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