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- PDB-353d: CRYSTAL STRUCTURE OF DOMAIN A OF THERMUS FLAVUS 5S RRNA AND THE C... -

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Basic information

Entry
Database: PDB / ID: 353d
TitleCRYSTAL STRUCTURE OF DOMAIN A OF THERMUS FLAVUS 5S RRNA AND THE CONTRIBUTION OF WATER MOLECULES TO ITS STRUCTURE
Components
  • RNA (5'-R(*AP*UP*CP*CP*CP*CP*CP*GP*UP*GP*CP*C)-3')
  • RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3')
KeywordsRNA / A-RNA / DOUBLE STRAND
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBetzel, C. / Lorenz, S. / Furste, J.P. / Bald, R. / Zhang, M. / Schneider, T.R. / Wilson, K.S. / Erdmann, V.A.
Citation
Journal: FEBS Lett. / Year: 1994
Title: Crystal structure of domain A of Thermus flavus 5S rRNA and the contribution of water molecules to its structure.
Authors: Betzel, C. / Lorenz, S. / Furste, J.P. / Bald, R. / Zhang, M. / Schneider, T.R. / Wilson, K.S. / Erdmann, V.A.
#1: Journal: To be Published
Title: Structure of Domain A of Thermus flavus 5S rRNA at 2.3 A Resolution. Comparison of Nearest Neighbor Parameters for Mismatches and the Influence of Solvent
Authors: Perbandt, M. / Lorenz, S. / Betzel, C. / Erdmann, V.A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Crystallization and Preliminary Diffraction Studies of the Chemically Synthesized Domain A of Thermus flavus 5S rRNA: An Dodecamer Double Helix
Authors: Lorenz, S. / Furste, J. / Bald, R. / Zhang, M. / Raderschall, E. / Betzel, C. / Dauter, Z. / Wilson, K.
History
DepositionSep 29, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 10, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Data collection / Experimental preparation / Category: diffrn / exptl_crystal_grow
Item: _diffrn.ambient_temp / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 2, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*AP*UP*CP*CP*CP*CP*CP*GP*UP*GP*CP*C)-3')
B: RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)7,6872
Polymers7,6872
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.100, 30.100, 86.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 3723.264 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3')


Mass: 3963.408 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5WATER12
6MPD12
7MGCL212
8NA CACODYLATE12
Crystal grow
*PLUS
Temperature: 45 ℃ / pH: 6.5
Details: Lorenz, S., (1993) Acta Crystallogr.,Sect.D, 49, 418.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlRNA1drop
25 %1drop
3200 mM1dropMgCl2
420 mMsodium cacodylate1drop
530 %MPD1reservoir
6400 mM1reservoirMgCl2
740 mMsodium cacodylate1reservoir
81

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11531
21531
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
SEALED TUBECONVENTIONAL Mo10.71070.7107
SYNCHROTRONEMBL/DESY, HAMBURG X1120.920.92
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
MARRESEARCH2IMAGE PLATE
Radiation
IDMonochromatorMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITEMx-ray1
2Mx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.71071
20.921
ReflectionHighest resolution: 2.4 Å / Num. obs: 2477 / % possible obs: 83.5 %
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 83.5 %

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Processing

Software
NameClassification
AMoREphasing
NUCLSQrefinement
XDSdata reduction
DENZOdata reduction
RefinementStarting model: NDB ENTRY ARN035 (PDB ENTRY 1RNA)

1rna


Resolution: 2.4→8 Å / σ(F): 0 / Details: X-PLOR (BRUNGER) ALSO WAS USED. /
RfactorNum. reflection
obs0.18 2477
Displacement parametersBiso mean: 23.9 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 508 0 158 666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.025
X-RAY DIFFRACTIONn_angle_d0.068
X-RAY DIFFRACTIONn_planar_d0.014
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr0.036
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
LS refinement shellResolution: 2.3→2.4 Å / % reflection obs: 50 %
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.025
X-RAY DIFFRACTIONn_angle_d0.068

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