+Open data
-Basic information
Entry | Database: PDB / ID: 3vfi | ||||||
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Title | Crystal Structure of a Metagenomic Thioredoxin | ||||||
Components | thioredoxin | ||||||
Keywords | ELECTRON TRANSPORT / Thioredoxin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Silicibacter phage DSS3phi2 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Craig, T.K. / Gardberg, A. / Lorimer, D.D. / Burgin Jr., A.B. / Segall, A. / Rohwer, F. | ||||||
Citation | Journal: To be Published Title: Structure of a Metagenomic Thioredoxin Authors: Craig, T.K. / Gardberg, A. / Lorimer, D.D. / Burgin Jr., A.B. / Segall, A. / Rohwer, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vfi.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vfi.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vfi_validation.pdf.gz | 423.1 KB | Display | wwPDB validaton report |
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Full document | 3vfi_full_validation.pdf.gz | 424.9 KB | Display | |
Data in XML | 3vfi_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 3vfi_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/3vfi ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vfi | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 12069.833 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Silicibacter phage DSS3phi2 (virus) / Plasmid: VCID_5533, pEMB31 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4NT42 |
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#2: 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: 1.89 Å3/Da / Density % sol: 34.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.44 Details: 0.27M Tris-HCL pH 8.44 13.52% (w/v) PEG 1000 13.52% (w/v) PEG 3350 13.52% (w/v) MPD 0.03M NaF 0.03M NaBr 0.03M NaI 0.4uL@ 10mg/mL + 0.4uL, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 19, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→50 Å / Num. all: 10095 / Num. obs: 9812 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.075 / Χ2: 1.025 / Net I/σ(I): 23.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 70.11 Å2 / Biso mean: 25.0787 Å2 / Biso min: 10.46 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7501→2.0031 Å
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