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- PDB-2ab3: Solution structures and characterization of HIV RRE IIB RNA targe... -

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Basic information

Entry
Database: PDB / ID: 2ab3
TitleSolution structures and characterization of HIV RRE IIB RNA targeting zinc finger proteins
ComponentsZNF29
KeywordsRNA BINDING PROTEIN / zinc finger protein / beta beta alpha / RREIIB-TR
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics
AuthorsMishra, S.H. / Shelley, C.M. / Darby, M.K. / Germann, M.W.
CitationJournal: Biopolymers / Year: 2006
Title: Solution structures and characterization of human immunodeficiency virus Rev responsive element IIB RNA targeting zinc finger proteins.
Authors: Mishra, S.H. / Shelley, C.M. / Barrow, D.J. / Darby, M.K. / Germann, M.W.
History
DepositionJul 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_nmr_software.name / _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
Remark 999 SEQUENCE THE SEQUENCE HAS NOT YET BEEN DEPOSITED IN ANY DATABASE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZNF29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6232
Polymers3,5571
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide ZNF29


Mass: 3557.146 Da / Num. of mol.: 1 / Fragment: Single Zinc Finger Protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Plasmid details: Designed zinc finger protein by Phage display
Plasmid: pET32b(+)Ek/Lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 plysS (Novagen)
#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
1112D NOESY
1212D TOCSY
131DQF-COSY
141E-COSY
15213 C HSQC
16315 N HSQC
173HMQC NOESY
183HMQC TOCSY
NMR detailsText: 13 C HSQC done at natural abundance

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM ZNF29; 10 mM phosphate buffer pH 6.8, 2mM Mercaptoethanol, 200 uM Sodium Azide, 50 uM Zinc Sulfate, 90% H2O, 10% D2O90% H2O/10% D2O
21.2 mM ZNF29; 10 mM phosphate buffer pH *6.4, 2mM Mercaptoethanol, 200 uM Sodium Azide, 50 uM Zinc Sulfate,"100%" D2O100% D2O
31.2 mM ZNF29 15N; 10 mM phosphate buffer pH 6.8, 2mM Mercaptoethanol, 200 uM Sodium Azide, 50 uM Zinc Sulfate, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: ~ 35 mM / pH: 6.8 / 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 AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Bruker Analytik GmbHcollection
Sparky3Goddard, T.D.data analysis
DYANA1.5Guentert, P.refinement
Amber7Case et alrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics
Software ordinal: 1
Details: The structure is based on a total of 316 restraints, 249 are NOE-derived distance restraints, 43 dihedral angle restraints, 16 distance restraints from hydrogen bonds, 8 distance constraints ...Details: The structure is based on a total of 316 restraints, 249 are NOE-derived distance restraints, 43 dihedral angle restraints, 16 distance restraints from hydrogen bonds, 8 distance constraints from coordinated Zinc ion.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1 / Conformers submitted total number: 1

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