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- PDB-1y9o: 1H NMR Structure of Acylphosphatase from the hyperthermophile Sul... -

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Basic information

Entry
Database: PDB / ID: 1y9o
Title1H NMR Structure of Acylphosphatase from the hyperthermophile Sulfolobus Solfataricus
ComponentsAcylphosphatase
KeywordsHYDROLASE / Sso / Acylphosphatase / Hyperthermophile
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity
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 speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / restrained minimization
AuthorsCorazza, A. / Rosano, C. / Pagano, K. / Alverdi, V. / Esposito, G. / Capanni, C. / Bemporad, F. / Plakoutsi, G. / Stefani, M. / Chiti, F. ...Corazza, A. / Rosano, C. / Pagano, K. / Alverdi, V. / Esposito, G. / Capanni, C. / Bemporad, F. / Plakoutsi, G. / Stefani, M. / Chiti, F. / Zuccotti, S. / Bolognesi, M. / Viglino, P.
Citation
Journal: Proteins / Year: 2006
Title: Structure, conformational stability, and enzymatic properties of acylphosphatase from the hyperthermophile Sulfolobus solfataricus
Authors: Corazza, A. / Rosano, C. / Pagano, K. / Alverdi, V. / Esposito, G. / Capanni, C. / Bemporad, F. / Plakoutsi, G. / Stefani, M. / Chiti, F. / Zuccotti, S. / Bolognesi, M. / Viglino, P.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Aggregation of the Acylphosphatase from Sulfolobus solfataricus: the folded and partially unfolded states can both be precursors for amyloid formation
Authors: Plakoutsi, G. / Taddei, N. / Stefani, M. / Chiti, F.
#2: Journal: Structure / Year: 1997
Title: Crystal structure of common type acylphosphatase from bovine testis
Authors: Thunnissen, M.M. / Taddei, N. / Liguri, G. / Ramponi, G. / Nordlund, P.
History
DepositionDec 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4May 29, 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


Theoretical massNumber of molelcules
Total (without water)11,7961
Polymers11,7961
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 / 20target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Acylphosphatase


Mass: 11796.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZL0, acylphosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
1422D TOCSY
1522D NOESY
162DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. Spectra were acquired within 36 hours from sample preparation.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM Sso AcP; 50mM phosphate buffer Na; 95% H2O, 5% D2O95% H2O/5% D2O
20.4mM Sso AcP; 50mM phosphate buffer Na; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 5.7 / Pressure: ambient / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker BioSpin GmbHcollection
XwinNMR2.6Bruker Analytik GmbHprocessing
Felix2000Krezel, A.M. et al.data analysis
CYANA1.0.6Guntert, P. et al.structure solution
Discover2.9.7refinement
RefinementMethod: restrained minimization / Software ordinal: 1
Details: restrained dihedral angle molecular dynamics simulation was performed by using the program CYANA. The 20 best structures of the CYANA ensemble were submitted to restrained minimization using ...Details: restrained dihedral angle molecular dynamics simulation was performed by using the program CYANA. The 20 best structures of the CYANA ensemble were submitted to restrained minimization using DISCOVER with the AMBER force field.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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