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- PDB-1nem: Saccharide-RNA recognition in the neomycin B / RNA aptamer complex -

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Basic information

Entry
Database: PDB / ID: 1nem
TitleSaccharide-RNA recognition in the neomycin B / RNA aptamer complex
Components5'-R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP*AP*GP*UP*CP*C)-3'
KeywordsRNA / RNA APTAMER / AMINOGLYCOSIDE / ANTIBIOTIC
Function / homology2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose / 2-DEOXY-D-STREPTAMINE / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE RESTRAINED MOLECULAR DYNAMICS
AuthorsJiang, L. / Majumdar, A. / Hu, W. / Jaishree, T.J. / Xu, W. / Patel, D.J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer
Authors: Jiang, L. / Majumdar, A. / Hu, W. / Jaishree, T.J. / Xu, W. / Patel, D.J.
History
DepositionMar 15, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _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 2.1Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP*AP*GP*UP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1114
Polymers7,4591
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)9 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: RNA chain 5'-R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP*AP*GP*UP*CP*C)-3'


Mass: 7459.481 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Complexed with neomycin B; hetero groups BDG (ring A), NEB (ring B), RIB (ring C), and NED (ring D)
#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-BDG / 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose / O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE / 2,6-diamino-2,6-dideoxy-alpha-D-glucose / 2,6-diamino-2,6-dideoxy-D-glucose / 2,6-diamino-2,6-dideoxy-glucose


Type: D-saccharide, alpha linking / Mass: 178.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14N2O4
IdentifierTypeProgram
DGlcpN[6N]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-GlcpN6NIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-NEB / 2-DEOXY-D-STREPTAMINE


Mass: 163.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O3 / Details: RING A OF NEOMYCIN B

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: EXPERIMENTS CONDUCTED IN D2O: 2D NOESY (50MS,120MS,200MS,300MS) PHASE-SENSITIVE COSY, TOCSY, (1H)- (13)C HSQC 3D (1H)-(13)C NOESY-HMQC (120MS, 300MS) 3D HCCH- COSY 3D HCCH-TOCSY 2D (1H)-(13)C ...Text: EXPERIMENTS CONDUCTED IN D2O: 2D NOESY (50MS,120MS,200MS,300MS) PHASE-SENSITIVE COSY, TOCSY, (1H)- (13)C HSQC 3D (1H)-(13)C NOESY-HMQC (120MS, 300MS) 3D HCCH- COSY 3D HCCH-TOCSY 2D (1H)-(13)C HCCH-TOCSY (65MS) 2D (1H)-(31)P CORRELATION 3D (1H)-(13)C-(31)P CORRELATION

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Sample preparation

Sample conditionsIonic strength: 10mM NA3PO4 / pH: 6.1 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementMethod: DISTANCE RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 9

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