+Open data
-Basic information
Entry | Database: PDB / ID: 3f9b | ||||||
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Title | W354F Yersinia enterocolitica PTPase complexed with divanadate | ||||||
Components | Tyrosine-protein phosphatase yopH | ||||||
Keywords | HYDROLASE / P-loop / WPD-loop / PTP / Protein Phosphatase / vanadate / divanadate / Membrane / Outer membrane / Secreted / Virulence | ||||||
Function / homology | Function and homology information dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | Yersinia enterocolitica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Brandao, T.A.S. / Robinson, H. / Johnson, S.J. / Hengge, A.C. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Impaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures. Authors: Brandao, T.A. / Robinson, H. / Johnson, S.J. / Hengge, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f9b.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f9b.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 3f9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f9b_validation.pdf.gz | 465.5 KB | Display | wwPDB validaton report |
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Full document | 3f9b_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 3f9b_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3f9b_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/3f9b ftp://data.pdbj.org/pub/pdb/validation_reports/f9/3f9b | HTTPS FTP |
-Related structure data
Related structure data | 3f99C 3f9aC 1yptS C: citing same article (ref.) S: Starting model for refinement |
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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: 33514.848 Da / Num. of mol.: 1 / Fragment: YopH catalytic domain: UNP residues 164-468 / Mutation: C235R, W354F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (type O:9) (bacteria) Strain: W22703 / Serotype O:9 / Biotype 2 / Gene: yopH, yop51 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15273, protein-tyrosine-phosphatase | ||
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#2: Chemical | ChemComp-VO4 / | ||
#3: Chemical | ChemComp-PDV / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Drop: 2uL of protein solution (20mg/mL in 100mM Sodium acetate, 100mM NaCl, 1mM EDTA, 1mM DTT, pH 5.7), 0.5uL of 55mM Sodium vanadate, and 3uL of precipitant solution (12-19% PEG 3350, 0.1M ...Details: Drop: 2uL of protein solution (20mg/mL in 100mM Sodium acetate, 100mM NaCl, 1mM EDTA, 1mM DTT, pH 5.7), 0.5uL of 55mM Sodium vanadate, and 3uL of precipitant solution (12-19% PEG 3350, 0.1M Hepes pH 7.5). Well: 1000uL of precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 19, 2008 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→30 Å / Num. all: 54027 / Num. obs: 54027 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.04 / Net I/σ(I): 30.828 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YPT Resolution: 1.42→29.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.173 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.893 / SU B: 1.86 / SU ML: 0.035 / SU R Cruickshank DPI: 0.074 / SU Rfree: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.063 / 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 max: 89.94 Å2 / Biso mean: 21.046 Å2 / Biso min: 11.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→29.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.46 Å / Total num. of bins used: 20
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