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- PDB-1wvo: Solution structure of RSGI RUH-029, an antifreeze protein like do... -

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Basic information

Entry
Database: PDB / ID: 1wvo
TitleSolution structure of RSGI RUH-029, an antifreeze protein like domain in human N-acetylneuraminic acid phosphate synthase gene.
ComponentsSialic acid synthase
KeywordsTRANSFERASE / Antifreeze protein like domain / N-Acetylneuraminic acid phosphate synthase / Structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


N-acylneuraminate-9-phosphate synthase / CMP-N-acetylneuraminate biosynthetic process / N-acetylneuraminate synthase / N-acetylneuraminate synthase activity / N-acylneuraminate-9-phosphate synthase activity / N-acylneuraminate cytidylyltransferase activity / glycosylation / Sialic acid metabolism / carbohydrate biosynthetic process / extracellular exosome ...N-acylneuraminate-9-phosphate synthase / CMP-N-acetylneuraminate biosynthetic process / N-acetylneuraminate synthase / N-acetylneuraminate synthase activity / N-acylneuraminate-9-phosphate synthase activity / N-acylneuraminate cytidylyltransferase activity / glycosylation / Sialic acid metabolism / carbohydrate biosynthetic process / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
N-acetylneuraminic acid synthase, N-terminal / : / NeuB family / SAF domain / SAF / SAF domain / Antifreeze, type III / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal ...N-acetylneuraminic acid synthase, N-terminal / : / NeuB family / SAF domain / SAF / SAF domain / Antifreeze, type III / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Aldolase-type TIM barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Sialic acid synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsIto, Y. / Hamada, T. / Hayashi, F. / Yokoyama, S. / Hirota, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2006
Title: Solution structure of the antifreeze-like domain of human sialic acid synthase
Authors: Hamada, T. / Ito, Y. / Abe, T. / Hayashi, F. / Guntert, P. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yoshida, M. / Tanaka, A. / Sugano, S. / Yokoyama, S. / Hirota, H.
History
DepositionDec 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2006Provider: 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_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 / _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: Sialic acid synthase


Theoretical massNumber of molelcules
Total (without water)8,2691
Polymers8,2691
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 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Sialic acid synthase / N-acetylneuraminate synthase / N-acetylneuraminic acid synthase / N-acetylneuraminate-9-phosphate ...N-acetylneuraminate synthase / N-acetylneuraminic acid synthase / N-acetylneuraminate-9-phosphate synthase / N-acetylneuraminic acid phosphate synthase


Mass: 8269.431 Da / Num. of mol.: 1 / Fragment: antifreeze protein like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P040531-08
References: UniProt: Q9NR45, N-acetylneuraminate synthase, N-acylneuraminate-9-phosphate synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: This structure was determined using 3D NMR techniques

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Sample preparation

DetailsContents: 1.1mM antifreeze protein like domain U-15N,13C; 20mM Tris-HCl buffer (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRPipe21_2Delaglio, F.collection
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9049Kobayashi, N.structure solution
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
OPALp1.4KORADI, R., BILLETER, M., GUNTERT, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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