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- PDB-1yws: Solution structure of YBL071w-A from Saccharomyces cerevisiae. -

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Basic information

Entry
Database: PDB / ID: 1yws
TitleSolution structure of YBL071w-A from Saccharomyces cerevisiae.
Componentsprotein YBL071w-A
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Zinc finger / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics
Function / homology
Function and homology information


2-(3-amino-3-carboxypropyl)histidine synthase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Synthesis of diphthamide-EEF2 / tRNA wobble uridine modification / iron chaperone activity / protein histidyl modification to diphthamide / ferrous iron binding / iron ion binding / zinc ion binding ...2-(3-amino-3-carboxypropyl)histidine synthase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Synthesis of diphthamide-EEF2 / tRNA wobble uridine modification / iron chaperone activity / protein histidyl modification to diphthamide / ferrous iron binding / iron ion binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Microbial ribonuclease fold / DPH Zinc finger / DPH-type metal-binding domain / DPH-type metal-binding domain superfamily / CSL zinc finger / DPH-type metal-binding (MB) domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
: / Diphthamide biosynthesis protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsLukin, J.A. / Guido, V. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Solution structure of YBL071w-A from Saccharomyces cerevisiae
Authors: Lukin, J.A. / Guido, V. / Arrowsmith, C.H.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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: protein YBL071w-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4262
Polymers9,3601
Non-polymers651
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
RepresentativeModel #19closest to the average

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Components

#1: Protein protein YBL071w-A


Mass: 9360.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YBL071w-A, KTI11 / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) GOLD MAGIC / References: GenBank: 21648335, UniProt: Q3E840*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM YBL071w-A, U-15N, U-13C; 450mM NaCl, 1mM benzamidine, 0.01% NaN3, 10mM MOPS, 0.01mM ZnSO4, 90% H2O, 10% D2O90% H2O/10% D2O
21mM YBL071w-A, U-15N, U-13C; 450mM NaCl, 1mM benzamidine, 0.01% NaN3, 10mM MOPS, 0.01mM ZnSO4, 99.9% D2O99.9% D2O
Sample conditionsIonic strength: 450mM NaCl / pH: 6.5 / 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
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio, F.processing
CYANA2Guentert, P. et al.structure solution
CNS1.1Brunger, A. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 100 structures were calculated by CYANA 2.0 using 1294 NOE-derived distance constraints, 122 dihedral angle constraints, and 54 distance constraints from hydrogen bonds. The 20 structures ...Details: 100 structures were calculated by CYANA 2.0 using 1294 NOE-derived distance constraints, 122 dihedral angle constraints, and 54 distance constraints from hydrogen bonds. The 20 structures with lowest target functions were subjected to refinement with CNS 1.1.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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