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Yorodumi- PDB-4xu5: Crystal structure of MvINS bound to a bromine-derived 14C Diacylg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xu5 | ||||||
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Title | Crystal structure of MvINS bound to a bromine-derived 14C Diacylglycerol (DAG) at 2.1A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION | ||||||
Function / homology | lipid binding / identical protein binding / membrane / DECANE / Chem-LBR / INSIG protein homolog Function and homology information | ||||||
Biological species | Mycobacterium vanbaalenii PYR-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Ren, R.B. / Wu, J.P. / Yan, C.Y. / He, Y. / Yan, N. | ||||||
Citation | Journal: Science / Year: 2015 Title: PROTEIN STRUCTURE. Crystal structure of a mycobacterial Insig homolog provides insight into how these sensors monitor sterol levels Authors: Ren, R. / Zhou, X. / He, Y. / Ke, M. / Wu, J. / Liu, X. / Yan, C. / Wu, Y. / Gong, X. / Lei, X. / Yan, S.F. / Radhakrishnan, A. / Yan, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xu5.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xu5.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xu5_validation.pdf.gz | 877.6 KB | Display | wwPDB validaton report |
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Full document | 4xu5_full_validation.pdf.gz | 881.8 KB | Display | |
Data in XML | 4xu5_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 4xu5_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/4xu5 ftp://data.pdbj.org/pub/pdb/validation_reports/xu/4xu5 | HTTPS FTP |
-Related structure data
Related structure data | 4xu4C 4xu6C 4xu7 4xu8 4xu9 C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21553.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium vanbaalenii PYR-1 (bacteria) Strain: PYR-1 / Gene: Mvan_1475 / Production host: Escherichia coli (E. coli) / References: UniProt: A1T557 | ||||
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#2: Chemical | ChemComp-LBR / ( | ||||
#3: Chemical | ChemComp-D10 / #4: Sugar | ChemComp-BOG / | #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: 3.88 Å3/Da / Density % sol: 68.28 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9185 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9185 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 37844 / % possible obs: 99.9 % / Redundancy: 4.1 % / Net I/σ(I): 20 |
-Processing
Software |
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Refinement | Resolution: 2.1→34.689 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.59 / Phase error: 19.76 / Stereochemistry target values: ML Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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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: 2.1→34.689 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 80.7332 Å / Origin y: 30.5871 Å / Origin z: -8.9642 Å
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Refinement TLS group | Selection details: all |