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Yorodumi- PDB-3dca: Crystal structure of the RPA0582- protein of unknown function fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dca | ||||||
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Title | Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target | ||||||
Components | RPA0582 | ||||||
Keywords | structural genomics / unknown function / Alpha-beta-barrel / SAD / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Domain of unknown function DUF1330 / Domain of unknown function (DUF1330) / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / DUF1330 domain-containing protein Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.35 Å | ||||||
Authors | Sledz, P. / Wang, S. / Chruszcz, M. / Yim, V. / Kudritska, M. / Evdokimova, E. / Turk, D. / Savchenko, A. / Edwards, A. / Joachimiak, A. ...Sledz, P. / Wang, S. / Chruszcz, M. / Yim, V. / Kudritska, M. / Evdokimova, E. / Turk, D. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target Authors: Sledz, P. / Wang, S. / Chruszcz, M. / Yim, V. / Kudritska, M. / Evdokimova, E. / Turk, D. / Savchenko, A. / Edwards, A. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dca.cif.gz | 103.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dca.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dca_validation.pdf.gz | 466.6 KB | Display | wwPDB validaton report |
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Full document | 3dca_full_validation.pdf.gz | 476.8 KB | Display | |
Data in XML | 3dca_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 3dca_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/3dca ftp://data.pdbj.org/pub/pdb/validation_reports/dc/3dca | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: THR / End label comp-ID: PRO / Refine code: 1 / Auth seq-ID: 2 - 133 / Label seq-ID: 2 - 133
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-Components
#1: Protein | Mass: 16269.880 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Gene: RPA0582 / Plasmid: P15TV LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90 #2: Chemical | ChemComp-SO4 / |
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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: 6.58 Å3/Da / Density % sol: 81.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M AMMONIUM SULPHATE, 0.1M NA CACODILATE PH6.5, 30%PEG8K, , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 / Wavelength: 0.979 Å | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2007 / Details: MIRROR | |||||||||
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.35→36.59 Å / Num. all: 22256 / Num. obs: 22256 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 98.16 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 13.716 | |||||||||
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 2 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2257 / Rsym value: 0.426 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.35→36.59 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.615 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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: 30.57 Å2
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Refinement step | Cycle: LAST / Resolution: 3.35→36.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1525 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05
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LS refinement shell | Resolution: 3.35→3.44 Å / Total num. of bins used: 20
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