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- PDB-1pbr: STRUCTURE OF 16S RIBOSOMAL RNA, NMR, MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1pbr
TitleSTRUCTURE OF 16S RIBOSOMAL RNA, NMR, MINIMIZED AVERAGE STRUCTURE
Components16S RIBOSOMAL RNA
KeywordsRNA / AMINOGLYCOSIDE / RIBOSOMAL RNA / RNA TRANSCRIPT / ANTIBIOTIC / RIBONUCLEIC ACID
Function / homology2-DEOXYSTREPTAMINE / 2-amino-2-deoxy-alpha-D-glucopyranose / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsFourmy, D. / Recht, M.I. / Blanchard, S. / Puglisi, J.D.
CitationJournal: Science / Year: 1996
Title: Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic.
Authors: Fourmy, D. / Recht, M.I. / Blanchard, S.C. / Puglisi, J.D.
History
DepositionSep 12, 1996Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2013Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3084
Polymers8,6561
Non-polymers6523
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: RNA chain 16S RIBOSOMAL RNA


Mass: 8656.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: NTS 1404/1412-1488/1497
#2: Polysaccharide 2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-beta-D-ribofuranose


Type: oligosaccharide / Mass: 310.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a222h-1b_1-4][a2121h-1b_1-5_2*N_6*N]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Ribf]{[(3+1)][b-L-IdopN6N]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-PA1 / 2-amino-2-deoxy-alpha-D-glucopyranose / alpah-D-glucosamine / 2-amino-2-deoxy-alpha-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose


Type: D-saccharide, alpha linking / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DGlcpNaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CYY / 2-DEOXYSTREPTAMINE


Mass: 162.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: 10MM NA PHOSPHATE

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Sample preparation

Sample conditionspH: 6.4 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: Discover / Developer: BIOSYM / Classification: refinement
NMR ensembleConformers submitted total number: 1

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