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Yorodumi- PDB-3gwh: Crystallographic Ab Initio protein solution far below atomic reso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gwh | ||||||
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Title | Crystallographic Ab Initio protein solution far below atomic resolution | ||||||
Components | Transcriptional antiterminator (BglG family) | ||||||
Keywords | TRANSCRIPTION / extended helix bundle / Ab Initio / Structure solution / ARCIMBOLDO / PHASER / SHELXE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 1.95 Å | ||||||
Authors | Rodriguez, D.D. / Grosse, C. / Himmel, S. / Gonzalez, C. / Becker, S. / Sheldrick, G.M. / Uson, I. | ||||||
Citation | Journal: Nat.Methods / Year: 2009 Title: Crystallographic ab initio protein structure solution below atomic resolution Authors: Rodriguez, D.D. / Grosse, C. / Himmel, S. / Gonzalez, C. / de Ilarduya, I.M. / Becker, S. / Sheldrick, G.M. / Uson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gwh.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gwh.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 3gwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gwh_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 3gwh_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 3gwh_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 3gwh_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/3gwh ftp://data.pdbj.org/pub/pdb/validation_reports/gw/3gwh | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13154.480 Da / Num. of mol.: 2 / Fragment: UNP residues 178-285 Source method: isolated from a genetically manipulated source Details: GST fusion protein, pGEX2TEV derived from commercial pGEX2T Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU13880, glcT / Plasmid: pGEX2TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O31691 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2.4M (NH4)2SO4, 0.1M citric acid, pH6.0, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Aug 22, 2008 / Details: MULTI-LAYER INCOATEC OPTICS |
Radiation | Monochromator: MULTI-LAYER INCOATEC OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35.98 Å / Num. obs: 12855 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 16.7 % / Rmerge(I) obs: 0.0906 / Net I/σ(I): 20.21 |
Reflection shell | Resolution: 1.95→2.04 Å / Redundancy: 1.75 % / Mean I/σ(I) obs: 2.45 / Num. unique all: 1786 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.95→35.98 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.837 / SU B: 4.629 / SU ML: 0.133 / SU R Cruickshank DPI: 0.214 / SU Rfree: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.214 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, The data were non-merohedrally twinned. The twinning fraction was 0.729/0.271, The data were detwinned with twinabs for refinement. The ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, The data were non-merohedrally twinned. The twinning fraction was 0.729/0.271, The data were detwinned with twinabs for refinement. The crystal was a two-component non-merohedral twin. The frames were indexed with CELL_NOW, integrated with SAINT and scaled with TWINABS (all programs from Bruker AXS) to obtain the merged intensities of the unique reflections from measurements of all 99947 reflections of domain 1, 98274 reflections of domain 2 and 25843 reflections for which both domains overlapped.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.6 Å2 / Biso mean: 27.144 Å2 / Biso min: 8.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→35.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.945→1.996 Å / Total num. of bins used: 20
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