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- PDB-2gv1: NMR solution structure of the Acylphosphatase from Eschaerichia Coli -

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Basic information

Entry
Database: PDB / ID: 2gv1
TitleNMR solution structure of the Acylphosphatase from Eschaerichia Coli
ComponentsProbable acylphosphatase
KeywordsHYDROLASE / globular alpha-helix/beta-sheet protein
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity / response to heat
Similarity search - Function
Acylphosphatase, bacteria / 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 ...Acylphosphatase, bacteria / 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 speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPagano, K. / Corazza, A. / Viglino, P. / Esposito, G.
Citation
Journal: J.Biomol.Nmr / Year: 2006
Title: NMR solution structure of the acylphosphatase from Escherichia coli.
Authors: Pagano, K. / Ramazzotti, M. / Viglino, P. / Esposito, G. / Degl'innocenti, D. / Taddei, N. / Corazza, A.
#1: 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.
#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.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Three-dimensional structure of acylphosphatase. Refinement and structure analysis.
Authors: Pastore, A. / Saudek, V. / Ramponi, G. / Williams, R.J.
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
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
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable acylphosphatase


Theoretical massNumber of molelcules
Total (without water)10,3151
Polymers10,3151
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 / 380target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Probable acylphosphatase / Acylphosphate phosphohydrolase


Mass: 10314.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yccX / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB65, acylphosphatase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D 15N HSQC
1523D 15N HSQC-NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy and standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate, 30 mM deuterated sodium acetate, 50 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
2U-15N, 50 mM sodium phosphate, 30 mM deuterated sodium acetate, 50 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 65 mM / pH: 4.95 / 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
XwinNMR2Bruker Biospincollection
XwinNMR2Bruker Biospinprocessing
CYANA2.1Guentert, 2003.structure solution
Discover2.9.7MSI, San Diego CArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1029 restraints, 970 are NOE-derived distance restraints and 59 dihedral angle restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 380 / Conformers submitted total number: 20

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