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Open data
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Basic information
Entry | Database: PDB / ID: 2p4u | ||||||
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Title | Crystal structure of acid phosphatase 1 (Acp1) from Mus musculus | ||||||
![]() | Acid phosphatase 1 | ||||||
![]() | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() acid phosphatase / acid phosphatase activity / phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / sarcolemma / SH3 domain binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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) | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.9 KB | Display | ![]() |
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PDB format | ![]() | 108.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469 KB | Display | ![]() |
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Full document | ![]() | 473 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 37.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data | |
Other databases |
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Links
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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
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Refinement | Method to determine structure: ![]() 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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