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- PDB-464d: DISORDER AND TWIN REFINEMENT OF RNA HEPTAMER DOUBLE HELIX -

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Basic information

Entry
Database: PDB / ID: 464d
TitleDISORDER AND TWIN REFINEMENT OF RNA HEPTAMER DOUBLE HELIX
Components
  • RNA (5'-R(*GP*GP*GP*GP*CP*(IU)P*A)-3')
  • RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
KeywordsRNA / 7 BASE-PAIR TRNA ALA ACCEPTOR STEM / DOUBLE HELIX / RIBONUCLEIC ACID / DISORDERED MODEL
Function / homologySTRONTIUM ION / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.23 Å
AuthorsMueller, U. / Muller, Y.A. / Herbst-Irmer, R. / Sprinzl, M. / Heinemann, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Disorder and twin refinement of RNA heptamer double helices.
Authors: Mueller, U. / Muller, Y.A. / Herbst-Irmer, R. / Sprinzl, M. / Heinemann, U.
History
DepositionApr 14, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 16, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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_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.ptnr1_label_seq_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 / _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: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*GP*CP*(IU)P*A)-3')
C: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*GP*CP*(IU)P*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2306
Polymers9,1194
Non-polymers1112
Water2,792155
1
A: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*GP*CP*(IU)P*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6704
Polymers4,5602
Non-polymers1112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*GP*CP*(IU)P*A)-3')


Theoretical massNumber of molelcules
Total (without water)4,5602
Polymers4,5602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.375, 28.995, 28.995
Angle α, β, γ (deg.)110.37, 96.62, 96.62
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

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


Mass: 2157.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE FROM TRNA(ALA) OF ESCHERICHIA COLI
#2: RNA chain RNA (5'-R(*GP*GP*GP*GP*CP*(IU)P*A)-3')


Mass: 2402.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE FROM TRNA(ALA) OF ESCHERICHIA COLI
#3: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.54 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.5 MM RNA DUPLEX, 12 MM SPERMINE, 40 MM NA-CACODYLATE PH 6.0, 80 MM SRCL2,40 MM LICL, 10 % (V/V) MPD AGAINST 0.5 ML 35 % (V/V) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1SPERMINE11
2SODIUM CACODYLATE11
3SRCL211
4LICL11
5MPD11
6MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMprotein1drop
240 mMsodium cacodylate1reservoir
312 mMspermine tetra-HCl1reservoir
480 mM1reservoirSrCl2
540 mM1reservoirLiCl
610 %(v/v)1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9049
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9049 Å / Relative weight: 1
ReflectionResolution: 1.23→15 Å / Num. all: 64180 / Num. obs: 64180 / % possible obs: 82.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.23→1.24 Å / Rmerge(I) obs: 0.308 / % possible all: 32.1
Reflection
*PLUS
Num. obs: 18837 / Num. measured all: 64180
Reflection shell
*PLUS
% possible obs: 32.1 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.23→15 Å / Num. parameters: 6709 / Num. restraintsaints: 21012 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 955 5.1 %THIN RESOLUTION SHELLS
Rwork0.127 ---
all0.129 18337 --
obs0.129 18337 96.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228
Refinement stepCycle: LAST / Resolution: 1.23→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 586 4 155 745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.029
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0.019
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.012
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.012
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.092
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5.1 % / Rfactor obs: 0.127 / Rfactor Rwork: 0.129
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.032

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