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Yorodumi- PDB-2bzl: CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE N14 A... -
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-Basic information
Entry | Database: PDB / ID: 2bzl | ||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE N14 AT 1. 65 A RESOLUTION | ||||||
Components | TYROSINE-PROTEIN PHOSPHATASE, NON-RECEPTOR TYPE 14 | ||||||
Keywords | HYDROLASE / PTPN14 / PROTEIN PHOSPHATASE | ||||||
Function / homology | Function and homology information lymphangiogenesis / regulation of protein export from nucleus / Interleukin-37 signaling / transcription coregulator activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / receptor tyrosine kinase binding / cytoskeleton / negative regulation of cell population proliferation ...lymphangiogenesis / regulation of protein export from nucleus / Interleukin-37 signaling / transcription coregulator activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / receptor tyrosine kinase binding / cytoskeleton / negative regulation of cell population proliferation / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Debreczeni, J.E. / Barr, A. / Eswaran, J. / Das, S. / Burgess, N. / Longman, E. / Fedorov, O. / Gileadi, O. / von Delft, F. / Sundstrom, M. ...Debreczeni, J.E. / Barr, A. / Eswaran, J. / Das, S. / Burgess, N. / Longman, E. / Fedorov, O. / Gileadi, O. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Knapp, S. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Crystal Structure of Human Protein Tyrosine Phosphatase 14 (Ptpn14) at 1.65-A Resolution. Authors: Barr, A.J. / Debreczeni, J.E. / Eswaran, J. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bzl.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bzl.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bzl_validation.pdf.gz | 455.4 KB | Display | wwPDB validaton report |
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Full document | 2bzl_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 2bzl_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 2bzl_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/2bzl ftp://data.pdbj.org/pub/pdb/validation_reports/bz/2bzl | HTTPS FTP |
-Related structure data
Related structure data | 1fprS 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: 37622.031 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 886-1187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC SGC / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q15678, protein-tyrosine-phosphatase | ||||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | BELONGS TO THE PROTEIN-TYROSINE PHOSPHATAS | Sequence details | RESIDUES 886-1187 CORRESPOND TO THE CATALYTIC DOMAIN OF OF THE PROTEIN, RESIDUES 863-885 ARE PART ...RESIDUES 886-1187 CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Method: vapor diffusion, sitting drop Details: SITTING DROP, 20% PEG3350, 0.2 M LI2SO4, 0.1 M BIS TRIS PROPANE PH 6.5, CRYO 20% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 2, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 41374 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.73 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.08 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.05 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FPR Resolution: 1.65→77.15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.067 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.092 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→77.15 Å
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