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Yorodumi- PDB-3c4r: Crystal structure of an uncharacterized protein encoded by crypti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c4r | ||||||
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Title | Crystal structure of an uncharacterized protein encoded by cryptic prophage | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / 10179a / uncharacterized protein / PSI-II / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | uncharacterized protein encoded by cryptic prophage fold / Putative bacterial toxin ydaT / Bacterial toxin YdaT / Bacterial toxin YdaT superfamily / Bacterial toxin ydaT / Orthogonal Bundle / Mainly Alpha / YdaT_toxin domain-containing protein / YdaT_toxin domain-containing protein Function and homology information | ||||||
Biological species | Escherichia coli O6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Sugadev, R. / Burley, S.K. / Swaminathan, S. / Ozyurt, S. / Luz, J. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an uncharacterized protein encoded by cryptic prophage. Authors: Sugadev, R. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c4r.cif.gz | 108.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c4r.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 3c4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c4r_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 3c4r_full_validation.pdf.gz | 468.2 KB | Display | |
Data in XML | 3c4r_validation.xml.gz | 21 KB | Display | |
Data in CIF | 3c4r_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c4r ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c4r | 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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-Components
#1: Protein | Mass: 17534.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6 (bacteria) / Species: Escherichia coli / Strain: O6:H1 / CFT073 / UPEC / Gene: c1411 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8FIL0, UniProt: A0A0H2V6G8*PLUS #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: 2.45 Å3/Da / Density % sol: 49.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Sodium cacodylate pH 5.5, 0.2M Magnesium acetate, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9795 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 2, 2007 / Details: SGX_CAT |
Radiation | Monochromator: SGX_CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 26286 / Num. obs: 26286 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1 / Num. unique all: 1744 / % possible all: 60 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→31.09 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 184194.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.8605 Å2 / ksol: 0.361853 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→31.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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