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Yorodumi- PDB-3fyf: Crystal structure of uncharacterized protein bvu_3222 from bacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fyf | ||||||
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Title | Crystal structure of uncharacterized protein bvu_3222 from bacteroides vulgatus | ||||||
Components | PROTEIN BVU-3222 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PERIPLASMIC / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM NYSGXRC / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS | ||||||
Function / homology | Protein of unknown function DUF4251 / Domain of unknown function (DUF4251) / Lipocalin - #410 / Lipocalin / Beta Barrel / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Bacteroides vulgatus ATCC 8482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Patskovsky, Y. / Bonanno, J.B. / Ozyurt, S. / Rutter, M. / Chang, S. / Groshong, C. / Koss, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Protein Bvu-3222 from Bacteroides Vulgatus Authors: Patskovsky, Y. / Bonanno, J.B. / Ozyurt, S. / Rutter, M. / Chang, S. / Groshong, C. / Koss, J. / Sauder, J.M. / 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 | 3fyf.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fyf.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fyf_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 3fyf_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 3fyf_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 3fyf_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fyf ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fyf | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS domain:
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Details | authors state that the biological unit is likely homodimer |
-Components
#1: Protein | Mass: 19503.549 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria) Gene: BVU-3222 / References: UniProt: A6L587 #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: 2.5 Å3/Da / Density % sol: 50.81 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200MM POTASSIUM CHLORIDE, PH 7.5, 20% PEG3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 8, 2008 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 19563 / % possible obs: 99 % / Observed criterion σ(I): -5 / Redundancy: 3.9 % / Biso Wilson estimate: 59.608 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.3 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.805 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.227 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.509 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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