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Yorodumi- PDB-3p42: Structure of GfcC (YmcB), protein encoded by the E. coli group 4 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p42 | ||||||
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Title | Structure of GfcC (YmcB), protein encoded by the E. coli group 4 capsule operon | ||||||
Components | Predicted protein | ||||||
Keywords | UNKNOWN FUNCTION / Beta-Grasp | ||||||
Function / homology | Function and homology information Ubiquitin-like (UB roll) - #700 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2280 / Capsule biosynthesis GfcC-like, C-terminal / Capsule biosynthesis GfcC C-terminal / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Ubiquitin-like (UB roll) ...Ubiquitin-like (UB roll) - #700 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2280 / Capsule biosynthesis GfcC-like, C-terminal / Capsule biosynthesis GfcC C-terminal / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Ubiquitin-like (UB roll) / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Escherichia coli O127:H6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Saper, M.A. / Sathiyamoorthy, K. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: The Crystal Structure of Escherichia coli Group 4 Capsule Protein GfcC Reveals a Domain Organization Resembling That of Wza. Authors: Sathiyamoorthy, K. / Mills, E. / Franzmann, T.M. / Rosenshine, I. / Saper, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p42.cif.gz | 523.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p42.ent.gz | 455 KB | Display | PDB format |
PDBx/mmJSON format | 3p42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p42_validation.pdf.gz | 460.7 KB | Display | wwPDB validaton report |
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Full document | 3p42_full_validation.pdf.gz | 469 KB | Display | |
Data in XML | 3p42_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 3p42_validation.cif.gz | 59.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/3p42 ftp://data.pdbj.org/pub/pdb/validation_reports/p4/3p42 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 26266.117 Da / Num. of mol.: 4 / Fragment: UNP residues 22-248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O127:H6 (bacteria) / Strain: E2348/69 / Gene: E2348C_0970, E2348_C_0970, gfcC / Plasmid: pETBlue2 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) pLacI / References: UniProt: B7UN63 #2: Chemical | #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: 2.26 Å3/Da / Density % sol: 45.56 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.5 M Ammonium Sulfate, 0.1 M NaCl, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9793 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2010 |
Radiation | Monochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→49 Å / Num. obs: 81677 / Redundancy: 6.8 % / Biso Wilson estimate: 25.01 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→34.494 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8582 / SU ML: 0.25 / σ(F): 0 / Phase error: 21.93 / Stereochemistry target values: ML Details: Refinement was with anomalous data, F+ and F- were refined as separate reflections.
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Solvent computation | Shrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.964 Å2 / ksol: 0.433 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 242.89 Å2 / Biso mean: 40.8623 Å2 / Biso min: 11.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→34.494 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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