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- PDB-1f1t: CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH T... -

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Basic information

Entry
Database: PDB / ID: 1f1t
TitleCRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE
ComponentsMALACHITE GREEN APTAMER RNA
KeywordsRNA / U-TURN / BASE QUADRUPLE / BASE TRIPLE / GNRA TETRALOOP / 5-BROMO-URIDINE
Function / homologyN,N'-TETRAMETHYL-ROSAMINE / STRONTIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsBaugh, C. / Grate, D. / Wilson, C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: 2.8 A crystal structure of the malachite green aptamer.
Authors: Baugh, C. / Grate, D. / Wilson, C.
History
DepositionMay 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALACHITE GREEN APTAMER RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,75610
Polymers12,7121
Non-polymers1,0449
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.297, 55.297, 143.92
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522

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Components

#1: RNA chain MALACHITE GREEN APTAMER RNA


Mass: 12711.902 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: IN VITRO T7 TRANSCRIPTION OF A LINEARIZED PLASMID TEMPLATE
#2: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-ROS / N,N'-TETRAMETHYL-ROSAMINE / (6-DIMETHYLAMINO-9-PHENYL-XANTHEN-3-YLIDENE)-DIMETHYL-AMMONIUM


Mass: 343.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: CACODYLATE, MGCL2, SRCL2, KCL, SPERMINE, MPD, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1CACODYLATE11
2MGCL211
3SRCL211
4KCL11
5SPERMINE11
6MPD11
7MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.33 %(v/v)MPD1drop
213.2 mMNa-cacodylate1drop
30.165 mMspermine1drop
423.16 mMKCl1drop
539.6 mM1dropSrCl2
66.66 mM1dropMgCl2
70.5 mMMGB RNA1drop
81 mMTMR1drop
935 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.92070, 0.92090, 0.90830, 1.0000
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 25, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92071
20.92091
30.90831
411
ReflectionResolution: 2.8→20 Å / Num. all: 3188 / Num. obs: 3188 / % possible obs: 99.7 % / Redundancy: 40.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 40.59
Reflection
*PLUS
Num. measured all: 128684

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→9 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.2822 -RANDOM
Rwork0.2609 --
obs0.2609 3188 -
all-3188 -
Refinement stepCycle: LAST / Resolution: 2.8→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 816 39 5 860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.96
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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