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- PDB-2k7k: Human Acylphosphatase (AcPh) common type -

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Basic information

Entry
Database: PDB / ID: 2k7k
TitleHuman Acylphosphatase (AcPh) common type
ComponentsAcylphosphatase-1
KeywordsHYDROLASE / PROTEIN / Acetylation
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity / phosphate-containing compound metabolic process
Similarity search - Function
Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits ...Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
AuthorsGribenko, A.V. / Patel, M.M. / Liu, J. / McCallum, S.A. / Wang, C. / Makhatadze, G.I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Rational stabilization of enzymes by computational redesign of surface charge-charge interactions
Authors: Gribenko, A.V. / Patel, M.M. / Liu, J. / McCallum, S.A. / Wang, C. / Makhatadze, G.I.
History
DepositionAug 13, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acylphosphatase-1


Theoretical massNumber of molelcules
Total (without water)11,2041
Polymers11,2041
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)20 / 100all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Acylphosphatase-1 / Acylphosphate phosphohydrolase 1 / Acylphosphatase / organ-common type isozyme / Acylphosphatase / ...Acylphosphate phosphohydrolase 1 / Acylphosphatase / organ-common type isozyme / Acylphosphatase / erythrocyte isozyme


Mass: 11203.696 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACYP1, ACYPE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysE / References: UniProt: P07311, acylphosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HN(CO)CA
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-15N TOCSY
11013D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.6 mM protein, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate1
50 mMsodium chloride1
Sample conditionsIonic strength: 50 / pH: 5.7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TopSpin2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 100 / Conformers submitted total number: 20

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