+Open data
-Basic information
Entry | Database: PDB / ID: 3fjm | ||||||
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Title | crystal structure of phosphate bound PEB3 | ||||||
Components | Major antigenic peptide PEB3 | ||||||
Keywords | TRANSPORT PROTEIN / PEB3 / phosphate. crystal structure | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Min, T. / Matte, A. / Cygler, M. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Specificity of Campylobacter jejuni adhesin PEB3 for phosphates and structural differences among its ligand complexes. Authors: Min, T. / Vedadi, M. / Watson, D.C. / Wasney, G.A. / Munger, C. / Cygler, M. / Matte, A. / Young, N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fjm.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fjm.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fjm_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 3fjm_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 3fjm_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 3fjm_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/3fjm ftp://data.pdbj.org/pub/pdb/validation_reports/fj/3fjm | HTTPS FTP |
-Related structure data
Related structure data | 3firC 3fj7C 3fjgC 2hxwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27711.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: 11168 / Gene: Cj0289c, peb3 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): AD202 / References: UniProt: Q0PBL7 #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: 2.22 Å3/Da / Density % sol: 44.47 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 18% [w/v] polyethylene glycol 3350, 0.2 M sodium phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 3, 2008 / Details: Vertical and Horizontal focusing Mirrors |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→18.7 Å / Num. obs: 65094 / % possible obs: 98 % / Redundancy: 6.6 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.067 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 8.1 / Num. unique all: 9228 / Rsym value: 0.277 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2hxw, PDB ENTRY peb3 Resolution: 1.6→18.7 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.595 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.096 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.385 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→18.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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