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Yorodumi- PDB-4r03: Crystal structure of a DUF3836 family protein (BDI_3222) from Par... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r03 | ||||||
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Title | Crystal structure of a DUF3836 family protein (BDI_3222) from Parabacteroides distasonis ATCC 8503 at 1.50 A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12930 family protein / DUF3836 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Lipocalin - #720 / Protein of unknown function DUF3836 / Family of unknown function (DUF3836) / Lipocalin / Beta Barrel / Mainly Beta / CITRIC ACID / PHOSPHATE ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Parabacteroides distasonis ATCC 8503 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Protein Sci. / Year: 2019 Title: Structures of single-layer beta-sheet proteins evolved from beta-hairpin repeats. Authors: Xu, Q. / Biancalana, M. / Grant, J.C. / Chiu, H.J. / Jaroszewski, L. / Knuth, M.W. / Lesley, S.A. / Godzik, A. / Elsliger, M.A. / Deacon, A.M. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r03.cif.gz | 41.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r03.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 4r03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r03_validation.pdf.gz | 456.6 KB | Display | wwPDB validaton report |
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Full document | 4r03_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 4r03_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 4r03_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/4r03 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/4r03 | HTTPS FTP |
-Related structure data
-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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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 13272.422 Da / Num. of mol.: 1 / Fragment: UNP residues 29-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria) Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_3222 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LGW3 | ||||
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#2: Chemical | ChemComp-MPD / ( | ||||
#3: Chemical | ChemComp-CIT / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 40.00% 2-methyl-2,4-pentanediol, 0.1M phosphate-citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97934,0.97907 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2014 Details: Vertical focusing mirror; double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→27.084 Å / Num. obs: 27948 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.114 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.96 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→27.084 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.175 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CITRATE (CIT), PHOSPHATE (PO4), AND 2-METHYL-2,4-PENTANEDIOL (MPD) WERE PRESENT IN PURIFICATION/CRYSTALLIZATION CONDITIONS.
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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 max: 74.87 Å2 / Biso mean: 22.887 Å2 / Biso min: 9.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→27.084 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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