+Open data
-Basic information
Entry | Database: PDB / ID: 4gio | ||||||
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Title | Crystal structure of Campylobacter jejuni cj0090 | ||||||
Components | Putative lipoprotein | ||||||
Keywords | UNKNOWN FUNCTION / LIPOPROTEIN | ||||||
Function / homology | Immunoglobulin-like - #3230 / Protein of unknown function DUF1425 / YcfL-like superfamily / Protein of unknown function (DUF1425) / Immunoglobulin-like / Sandwich / Mainly Beta / BROMIDE ION / Putative lipoprotein Function and homology information | ||||||
Biological species | Campylobacter jejuni subsp. jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Kawai, F. / Yeo, H.J. | ||||||
Citation | Journal: Proteins / Year: 2012 Title: Crystal structure of the Campylobacter jejuni Cj0090 protein reveals a novel variant of the immunoglobulin fold among bacterial lipoproteins. Authors: Paek, S. / Kawai, F. / Choi, K.J. / Yeo, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gio.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gio.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gio_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
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Full document | 4gio_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 4gio_validation.xml.gz | 11 KB | Display | |
Data in CIF | 4gio_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/4gio ftp://data.pdbj.org/pub/pdb/validation_reports/gi/4gio | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12307.028 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 16-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: NCTC 11168 / Gene: Cj0090 / Plasmid: PET45B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0PC47 #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: 2.48 Å3/Da / Density % sol: 50.44 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES, PH 7.0, 0.8M NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2010 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 19705 / % possible obs: 95.5 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.313 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→19.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.601 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R Free: 0.142 / 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: 25.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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