+Open data
-Basic information
Entry | Database: PDB / ID: 4ryo | ||||||
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Title | Crystal structure of BcTSPO type II high resolution monomer | ||||||
Components | Integral membrane protein | ||||||
Keywords | MEMBRANE PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS / Receptor | ||||||
Function / homology | Function and homology information tetrapyrrole metabolic process / tetrapyrrole binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Guo, Y. / Liu, Q. / Hendrickson, W.A. / New York Consortium on Membrane Protein Structure (NYCOMPS) | ||||||
Citation | Journal: Science / Year: 2015 Title: Protein structure. Structure and activity of tryptophan-rich TSPO proteins. Authors: Guo, Y. / Kalathur, R.C. / Liu, Q. / Kloss, B. / Bruni, R. / Ginter, C. / Kloppmann, E. / Rost, B. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ryo.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ryo.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ryo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ryo_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4ryo_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4ryo_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 4ryo_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/4ryo ftp://data.pdbj.org/pub/pdb/validation_reports/ry/4ryo | HTTPS FTP |
-Related structure data
Related structure data | 4ryiC 4ryjC 4rymC 4rynC 4ryqC 4ryrC 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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-Components
#1: Protein | Mass: 21496.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_3136, DSM 31 / Plasmid: pMCSG7 10xHis 30021246 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81BL7 | ||||
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#2: Chemical | ChemComp-MPG / [( #3: Chemical | ChemComp-DMS / #4: 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: 1.97 Å3/Da / Density % sol: 37.48 % |
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Crystal grow | Temperature: 293 K / pH: 5.5 Details: crystals grew from 0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v polyethylene glycol 3,350 in LCP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9791 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 10, 2014 |
Radiation | Monochromator: SINGLE CRYSTAL BENDER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 5354 / % possible obs: 94.3 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.6→1.73 Å / % possible all: 81.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.94 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 26.22 / 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: 1.6→29.94 Å
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Refine LS restraints |
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LS refinement shell |
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