+Open data
-Basic information
Entry | Database: PDB / ID: 2p4u | ||||||
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Title | Crystal structure of acid phosphatase 1 (Acp1) from Mus musculus | ||||||
Components | Acid phosphatase 1 | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sarcolemma / cytoplasmic side of plasma membrane / SH3 domain binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bonanno, J.B. / Freeman, J. / Bain, K.T. / Wu, B. / Xu, W. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2007 Title: Structural genomics of protein phosphatases. Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p4u.cif.gz | 138.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p4u.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 2p4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p4u ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p4u | HTTPS FTP |
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-Related structure data
Related structure data | 1rxdC 2fh7C 2g59C 2hcmC 2hhlC 2hxpC 2hy3C 2i0oC 2i1yC 2i44C 2iq1C 2irmC 2isnC 2nv5C 2oycC 2p27C 2p69C 2p8eC 2pbnC 2q5eC 2qjcC 2r0bC 1xwwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19160.674 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: FVB/N / Gene: Acp1 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q561M1, UniProt: Q9D358*PLUS, acid phosphatase #2: Chemical | ChemComp-PO4 / #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: 2.01 Å3/Da / Density % sol: 38.67 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion Details: 10mM Sodium acetate, 70% MPD, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 9, 2007 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 49330 / Num. obs: 48689 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.116 / Χ2: 2.377 / Net I/σ(I): 19.09 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4836 / Χ2: 0.816 / % possible all: 98.4 |
-Phasing
Phasing MR | Rfactor: 0.532 / Cor.coef. Fo:Fc: 0.292
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XWW Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.524 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.705 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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