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- PDB-2l77: Solution NMR structure of PAP248-286 in 50% TFE -

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Basic information

Entry
Database: PDB / ID: 2l77
TitleSolution NMR structure of PAP248-286 in 50% TFE
ComponentsProstatic acid phosphatase
KeywordsHYDROLASE / PAP248-286 / SEVI / AMYLOID
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 / regulation of sensory perception of pain / acid phosphatase / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / regulation of sensory perception of pain / acid phosphatase / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / choline binding / nucleotide metabolic process / vesicle membrane / azurophil granule membrane / dephosphorylation / lysosome organization / phosphatase activity / purine nucleobase metabolic process / multivesicular body / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / filopodium / 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
Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
Prostatic acid phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsfewest violations, model 1
AuthorsNanga, R. / Brender, J.R. / Popovych, N. / Ramamoorthy, A.
CitationJournal: To be Published
Title: Solution NMR structure of PAP248-286 in TFE
Authors: Brender, J.R. / Nanga, R. / Popovych, N. / Soong, R. / MacDonald, P.M. / Ramamoorthy, A.
History
DepositionDec 3, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostatic acid phosphatase


Theoretical massNumber of molelcules
Total (without water)4,5611
Polymers4,5611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Prostatic acid phosphatase / PAP


Mass: 4561.464 Da / Num. of mol.: 1 / Fragment: UNP residues 248-286 / Source method: obtained synthetically / Details: purchased from from a vendor / Source: (synth.) Homo sapiens (human) / References: UniProt: P15309, acid phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.2 mM PAP248-286-1; 20 mM sodium phosphate-2; 10 % [U-99% 2H] D2O-3; 50 % [U-99% 2H] TFE-4; trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMPAP248-286-11
20 mMsodium phosphate-21
10 %D2O-3[U-99% 2H]1
50 %TFE-4[U-99% 2H]1
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
TALOSCornilescu, Delaglio and Baxrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
MOLMOLKoradi, Billeter and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
ProcheckNMRLaskowski and MacArthurstructure solution
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000 / Conformers submitted total number: 10 / Representative conformer: 1

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