+Open data
-Basic information
Entry | Database: PDB / ID: 2qsd | ||||||
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Title | Crystal structure of a protein Il1583 from Idiomarina loihiensis | ||||||
Components | Uncharacterized conserved protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information protein il1583 fold / protein il1583 domain / Domain of unknown function DUF1543 / Domain of Unknown Function (DUF1543) / Ubiquitin-like (UB roll) - #10 / 3-Layer(bba) Sandwich / Ubiquitin-like (UB roll) / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Idiomarina loihiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Patskovsky, Y. / Bonanno, J. / Sauder, J.M. / Romero, R. / Rutter, M. / Koss, J. / Mckenzie, C. / Gheyi, T. / Bain, K. / Wasserman, S.R. ...Patskovsky, Y. / Bonanno, J. / Sauder, J.M. / Romero, R. / Rutter, M. / Koss, J. / Mckenzie, C. / Gheyi, T. / Bain, K. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a Protein Il1583 from Idiomarina loihiensis. Authors: Patskovsky, Y. / Bonanno, J. / Sauder, J.M. / Romero, R. / Rutter, M. / Koss, J. / Mckenzie, C. / Gheyi, T. / Bain, K. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qsd.cif.gz | 246.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qsd.ent.gz | 206.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qsd_validation.pdf.gz | 499.2 KB | Display | wwPDB validaton report |
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Full document | 2qsd_full_validation.pdf.gz | 509.5 KB | Display | |
Data in XML | 2qsd_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 2qsd_validation.cif.gz | 59.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/2qsd ftp://data.pdbj.org/pub/pdb/validation_reports/qs/2qsd | 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: ASP / End label comp-ID: HOH / Refine code: 1 / Auth seq-ID: 5 - 200 / Label seq-ID: 7
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Details | homodimer, ASU contains 8 monomers assembled as 4 dimers, AB,ED,CG,FH |
-Components
#1: Protein | Mass: 21358.574 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Idiomarina loihiensis (bacteria) / Strain: L2-TR, DSM 15497 / Gene: IL1583 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5QU98 #2: Chemical | ChemComp-GOL / | #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: 3.11 Å3/Da / Density % sol: 60.43 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2M Ammonium sulfate, 0.1M Tris-HCl, 10% Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 24, 2007 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 142014 / % possible obs: 99.8 % / Observed criterion σ(I): -0.5 / Redundancy: 5.7 % / Biso Wilson estimate: 70.85 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.059 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.794 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The Bijvoet differences were used for phasing. 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.717 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1142 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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