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Yorodumi- PDB-2p12: Crystal structure of protein of unknown function DUF402 from Rhod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p12 | ||||||
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Title | Crystal structure of protein of unknown function DUF402 from Rhodococcus sp. RHA1 | ||||||
Components | Hypothetical protein DUF402Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC7392 / beta-barrel / Rhodococcus sp. RHA1 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | Function and homology information Uncharacterised conserved protein UCP012622 / FomD barrel-like fold / FomD-like / Domain of unknown function DUF402 / FomD-like superfamily / Protein of unknown function (DUF402) / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å | ||||||
Authors | Kim, Y. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the protein of uncharacterized function, DUF402 from Rhodococcus sp. RHA1 Authors: Kim, Y. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p12.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p12.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 2p12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/2p12 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/2p12 | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20351.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: RHA1_ro00977 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0SI31 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.13 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97916 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2007 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→40.3 Å / Num. all: 40684 / Num. obs: 40684 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.54 / Num. unique all: 2264 / % possible all: 52 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.63→40.3 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.283 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.116 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.495 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→40.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.672 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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