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Open data
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Basic information
Entry | Database: PDB / ID: 3bd0 | ||||||
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Title | Crystal structure of Memo, form II | ||||||
![]() | Protein MEMO1 | ||||||
![]() | PEPTIDE BINDING PROTEIN / alpha/beta structure | ||||||
Function / homology | ![]() regulation of microtubule-based process / ERBB2 Regulates Cell Motility / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qiu, C. | ||||||
![]() | ![]() Title: Memo Is Homologous to Nonheme Iron Dioxygenases and Binds an ErbB2-derived Phosphopeptide in Its Vestigial Active Site. Authors: Qiu, C. / Lienhard, S. / Hynes, N.E. / Badache, A. / Leahy, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.6 KB | Display | ![]() |
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PDB format | ![]() | 188.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465 KB | Display | ![]() |
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Full document | ![]() | 485.4 KB | Display | |
Data in XML | ![]() | 42 KB | Display | |
Data in CIF | ![]() | 57.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bczSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 2 / Auth seq-ID: 5 - 297 / Label seq-ID: 1 - 293
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Components
#1: Protein | Mass: 33284.582 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PEG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystal was grown in 22.5% PEG 3350, 0.1 M MES pH 5.5. Soaked in 5 mM ZnCl2, 22.5% PEG 3350 pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97989 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→30 Å / Num. obs: 24559 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.227 / Χ2: 0.939 / Net I/σ(I): 3.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3BCZ Resolution: 3.01→29.68 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.811 / SU B: 21.523 / SU ML: 0.402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.546 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.753 Å2
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Refinement step | Cycle: LAST / Resolution: 3.01→29.68 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.01→3.08 Å / Total num. of bins used: 20
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