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Yorodumi- PDB-4z9a: Crystal structure of Low Molecular Weight Protein Tyrosine Phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z9a | |||||||||||||||
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Title | Crystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with phenylmethanesulfonic acid | |||||||||||||||
Components | Low molecular weight phosphotyrosine protein phosphatase | |||||||||||||||
Keywords | HYDROLASE / Protein Tyrosine Phosphatase / protein-ligand complex / phenylmethanesulfonic acid | |||||||||||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sarcolemma / cytoplasmic side of plasma membrane / extracellular exosome / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||||||||
Authors | Trivella, D.B.B. / Fonseca, E.M.B. / Scorsato, V. / Dias, M.P. / Aparicio, R. | |||||||||||||||
Funding support | Brazil, 4items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2015 Title: Crystal structures of the apo form and a complex of human LMW-PTP with a phosphonic acid provide new evidence of a secondary site potentially related to the anchorage of natural substrates. Authors: Fonseca, E.M. / Trivella, D.B. / Scorsato, V. / Dias, M.P. / Bazzo, N.L. / Mandapati, K.R. / de Oliveira, F.L. / Ferreira-Halder, C.V. / Pilli, R.A. / Miranda, P.C. / Aparicio, R. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z9a.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z9a.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 4z9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/4z9a ftp://data.pdbj.org/pub/pdb/validation_reports/z9/4z9a | HTTPS FTP |
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-Related structure data
Related structure data | 4z99C 4z9bC 5pntS 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: 18755.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 References: UniProt: P24666, protein-tyrosine-phosphatase, acid phosphatase | ||||
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#2: Chemical | ChemComp-GOL / | ||||
#3: Chemical | #4: Chemical | ChemComp-PMS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 26% (w/v) PEG 5000, 0.2 M ammonium sulfate, 0.2 M MES buffer pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→32.6 Å / Num. obs: 10699 / % possible obs: 98.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.2 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5PNT Resolution: 2.1→28.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.831 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.19 / 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: 41.696 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→28.07 Å
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Refine LS restraints |
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