+Open data
-Basic information
Entry | Database: PDB / ID: 5eog | ||||||
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Title | Structure of full-length human MAB21L1 | ||||||
Components | Protein mab-21-like 1 | ||||||
Keywords | TRANSFERASE / Nucleotidyltransferase fold protein | ||||||
Function / homology | Function and homology information eye development / camera-type eye development / anatomical structure morphogenesis / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / cell population proliferation / positive regulation of cell population proliferation / GTP binding / ATP binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | de Oliveira Mann, C.C. / Witte, G. / Hopfner, K.-P. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: Structural and biochemical characterization of the cell fate determining nucleotidyltransferase fold protein MAB21L1. Authors: de Oliveira Mann, C.C. / Kiefersauer, R. / Witte, G. / Hopfner, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eog.cif.gz | 675.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eog.ent.gz | 572.9 KB | Display | PDB format |
PDBx/mmJSON format | 5eog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/5eog ftp://data.pdbj.org/pub/pdb/validation_reports/eo/5eog | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 41259.617 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAB21L1, CAGR1, Nbla00126 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13394 #2: Chemical | ChemComp-CIT / #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: 3.59 Å3/Da / Density % sol: 65.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1M Trisodium citrate 0.1M MES / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. obs: 50759 / % possible obs: 98.8 % / Redundancy: 7 % / Rsym value: 0.044 / Net I/σ(I): 22.51 |
Reflection shell | Resolution: 3.05→3.13 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 1.157 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: initial model from Se-SAD Resolution: 3.05→48.592 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→48.592 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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