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Yorodumi- PDB-4pup: 2.75 Angstrom resolution crystal structure of uncharacterized pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pup | ||||||
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Title | 2.75 Angstrom resolution crystal structure of uncharacterized protein from Burkholderia cenocepacia J2315 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / Burkholderia cenocepacia J2315 / APC110287 | ||||||
Function / homology | NinX, bacteriophage P22 / Bacteriophage P22, NinX / DUF2591 domain-containing protein Function and homology information | ||||||
Biological species | Burkholderia cenocepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å | ||||||
Authors | Halavaty, A.S. / Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Minasov, G. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: 2.75 Angstrom resolution crystal structure of uncharacterized protein from Burkholderia cenocepacia J2315 Authors: Halavaty, A.S. / Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Minasov, G. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pup.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pup.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pup_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 4pup_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 4pup_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4pup_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/4pup ftp://data.pdbj.org/pub/pdb/validation_reports/pu/4pup | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 14239.280 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BCAM1129 / Plasmid: pMCSG87 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: B4EGA9 #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: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: protein: 7 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME, crystallization conditions: 0.2 M Sodium formate, 20 % (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2014 / Details: Be lenses |
Radiation | Monochromator: Diamond / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. all: 10997 / Num. obs: 10997 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.605 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.75→28.64 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.912 / SU B: 32.202 / SU ML: 0.298 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 4.067 / ESU R Free: 0.357 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.312 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→28.64 Å
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Refine LS restraints |
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