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Yorodumi- PDB-3gnj: The crystal structure of a thioredoxin-related protein from Desul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gnj | ||||||
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Title | The crystal structure of a thioredoxin-related protein from Desulfitobacterium hafniense DCB | ||||||
Components | Thioredoxin domain protein | ||||||
Keywords | structural genomics / unknown function / APC92103 / thioredoxin / Desulfitobacterium hafniense DCB / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Thioredoxin domain protein Function and homology information | ||||||
Biological species | Desulfitobacterium hafniense DCB-2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å | ||||||
Authors | Tan, K. / Volkart, L. / Gu, M. / Kinney, J.N. / Babnigg, G. / Kerfeld, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a thioredoxin-related protein from Desulfitobacterium hafniense DCB Authors: Tan, K. / Volkart, L. / Gu, M. / Kinney, J.N. / Babnigg, G. / Kerfeld, C. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gnj.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gnj.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 3gnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gnj ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gnj | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | Experimentally unknown. It is predicted that the chains A and B, C and D form dimers respectively. |
-Components
#1: Protein | Mass: 13127.140 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense DCB-2 (bacteria) Strain: DCB / Gene: Desulfitobacterium hafniense, Dhaf_4889 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: B8G0E7 #2: 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: 1.84 Å3/Da / Density % sol: 33.23 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG400 0.1M MES, 0.1M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921, 0.97942 | |||||||||
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 8, 2008 / Details: mirror | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.99→26 Å / Num. all: 26104 / Num. obs: 26104 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 22.6 | |||||||||
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.3 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.99→25.92 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.343 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→25.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.986→2.037 Å / Total num. of bins used: 20
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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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