+Open data
-Basic information
Entry | Database: PDB / ID: 1cvi | |||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN PROSTATIC ACID PHOSPHATASE | |||||||||
Components | PROSTATIC ACID PHOSPHATASE | |||||||||
Keywords | HYDROLASE / ACID PHOSPHATASE / INHIBITION | |||||||||
Function / homology | Function and homology information 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 / nucleotide metabolic process / choline binding / vesicle membrane / azurophil granule membrane / lysosome organization / dephosphorylation / phosphatase activity / purine nucleobase metabolic process / multivesicular body / protein-tyrosine-phosphatase / filopodium / protein tyrosine phosphatase activity / lipid metabolic process / apical part of cell / molecular adaptor activity / lysosome / lysosomal membrane / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3.2 Å | |||||||||
Authors | Jakob, C.G. / Lewinski, K. / Kuciel, R. / Ostrowski, W. / Lebioda, L. | |||||||||
Citation | Journal: Prostate / Year: 2000 Title: Crystal structure of human prostatic acid phosphatase . Authors: Jakob, C.G. / Lewinski, K. / Kuciel, R. / Ostrowski, W. / Lebioda, L. #1: Journal: J.Biol.Chem. / Year: 1998 Title: Structural Origins of L(+)-Tartarate Inhibition of Human Prostatic Acid Phosphatase Authors: Lacount, M.W. / Handy, G. / Lebioda, L. #2: Journal: Acta Biochim.Pol. / Year: 1997 Title: Prostatic Acid Phosphatase: Structural Aspects of Inhibition by L-(+)-Tartarate Ions Authors: Lovelace, L. / Lewinski, K. / Jakob, C.G. / Kuciel, R. / Ostrowski, W. / Lebioda, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cvi.cif.gz | 310.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cvi.ent.gz | 257.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cvi_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1cvi_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1cvi_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 1cvi_validation.cif.gz | 55.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/1cvi ftp://data.pdbj.org/pub/pdb/validation_reports/cv/1cvi | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39776.426 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: SEMINAL FLUID / References: UniProt: P15309, acid phosphatase |
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-Sugars , 6 types, 12 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 | ||||||
#4: 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 #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 #7: Sugar | |
-Non-polymers , 2 types, 637 molecules
#8: Chemical | ChemComp-GLY / #9: 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: 3.01 Å3/Da / Density % sol: 59.17 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 10 Details: PEG 1450, POTASSIUM CHLORIDE, GLYCINE, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 15, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.16→80.28 Å / Num. all: 30755 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 3.16→3.5 Å / % possible all: 82.1 |
Reflection | *PLUS Num. obs: 30755 |
-Processing
Software |
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Refinement | Resolution: 3.2→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 45.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.39 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 6.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 45.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.323 / % reflection Rfree: 6.5 % / Rfactor Rwork: 0.214 |