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- PDB-1yop: The solution structure of Kti11p -

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Basic information

Entry
Database: PDB / ID: 1yop
TitleThe solution structure of Kti11p
ComponentsKti11p
KeywordsMETAL BINDING PROTEIN / zinc finger
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 / iron chaperone activity / protein histidyl modification to diphthamide / tRNA wobble uridine modification / 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 / iron chaperone activity / protein histidyl modification to diphthamide / tRNA wobble uridine modification / ferrous iron binding / iron ion binding / zinc ion binding / nucleus / cytosol / cytoplasm
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
AuthorsSun, J. / Zhang, J. / Wu, F. / Xu, C. / Li, S. / Zhao, W. / Wu, Z. / Wu, J. / Zhou, C.-Z. / Shi, Y.
CitationJournal: Biochemistry / Year: 2005
Title: Solution structure of Kti11p from Saccharomyces cerevisiae reveals a novel zinc-binding module.
Authors: Sun, J. / Zhang, J. / Wu, F. / Xu, C. / Li, S. / Zhao, W. / Wu, Z. / Wu, J. / Zhou, C.Z. / Shi, Y.
History
DepositionJan 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Kti11p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5252
Polymers9,4601
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 / 100structures with the lowest energy
RepresentativeModel #19closest to the average

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Components

#1: Protein Kti11p


Mass: 9459.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: Q3E840
#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 detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 20mM Tris buffer, 50mM NaCl / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 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 spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeF. Delaglio, S. Grzesiek et alprocessing
CNS1refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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