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- PDB-1rpa: THREE-DIMENSIONAL STRUCTURE OF RAT ACID PHOSPHATASE IN COMPLEX WI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rpa | |||||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF RAT ACID PHOSPHATASE IN COMPLEX WITH L(+) TARTRATE | |||||||||
![]() | PROSTATIC ACID PHOSPHATASE | |||||||||
![]() | HYDROLASE(PHOSPHORIC MONOESTER) | |||||||||
Function / homology | ![]() thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / XMP 5'-nucleosidase activity / acid phosphatase activity ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / XMP 5'-nucleosidase activity / acid phosphatase activity / 5'-nucleotidase / 5'-nucleotidase activity / vesicle membrane / nucleotide metabolic process / choline binding / Neutrophil degranulation / lysosome organization / phosphatase activity / purine nucleobase metabolic process / dephosphorylation / multivesicular body / protein-tyrosine-phosphatase / secretory granule / protein tyrosine phosphatase activity / filopodium / lipid metabolic process / apical part of cell / molecular adaptor activity / lysosome / lysosomal membrane / protein homodimerization activity / extracellular space / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Lindqvist, Y. / Schneider, G. | |||||||||
![]() | ![]() Title: Three-dimensional structure of rat acid phosphatase in complex with L(+)-tartrate. Authors: Lindqvist, Y. / Schneider, G. / Vihko, P. #1: ![]() Title: Three-Dimensional Structure of Rat Acid Phosphatase Authors: Schneider, G. / Lindqvist, Y. / Vihko, P. #2: ![]() Title: Rat Acid Phosphatase: Overexpression of Active, Secreted Enzyme by Recombinant Baculovirus-Infected Insect Cells, Molecular Properties, and Crystallization Authors: Vihko, P. / Kurkela, R. / Porvari, K. / Herrala, A. / Lindfors, A. / Lindqvist, Y. / Schneider, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.9 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 499.5 KB | Display | ![]() |
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Full document | ![]() | 525.8 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 125 2: GLN 244 - PRO 245 OMEGA =235.93 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
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Components
#1: Protein | Mass: 39691.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Chemical | ChemComp-TAR / |
Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 72.14 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Num. obs: 11350 / % possible obs: 80 % / Num. measured all: 24008 / Rmerge(I) obs: 0.057 |
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Processing
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Refinement | Rfactor Rwork: 0.215 / Rfactor obs: 0.215 / Highest resolution: 3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Rfactor obs: 0.215 / Rfactor Rwork: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 4 |