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- PDB-1dgz: RIBOSMAL PROTEIN L36 FROM THERMUS THERMOPHILUS: NMR STRUCTURE ENSEMBLE -

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Basic information

Entry
Database: PDB / ID: 1dgz
TitleRIBOSMAL PROTEIN L36 FROM THERMUS THERMOPHILUS: NMR STRUCTURE ENSEMBLE
ComponentsPROTEIN (L36 RIBOSOMAL PROTEIN)
KeywordsRIBOSOME / RIBOSOMAL PROTEIN / LARGE RIBOSOMAL SUBUNIT / ZINC BINDING / BETA SHEET
Function / homology
Function and homology information


structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L36 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36
Similarity search - Domain/homology
Large ribosomal subunit protein bL36
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR
AuthorsHard, T. / Rak, A. / Allard, P. / Kloo, L. / Garber, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The solution structure of ribosomal protein L36 from Thermus thermophilus reveals a zinc-ribbon-like fold.
Authors: Hard, T. / Rak, A. / Allard, P. / Kloo, L. / Garber, M.
History
DepositionNov 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 (L36 RIBOSOMAL PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5012
Polymers4,4351
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)38 / 50STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON- BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #7

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Components

#1: Protein/peptide PROTEIN (L36 RIBOSOMAL PROTEIN)


Mass: 4435.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P80256
#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

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON- BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 38

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