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- PDB-361d: CRYSTAL STRUCTURE OF DOMAIN E OF THERMUS FLAVUS 5S RRNA: A HELICA... -

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Basic information

Entry
Database: PDB / ID: 361d
TitleCRYSTAL STRUCTURE OF DOMAIN E OF THERMUS FLAVUS 5S RRNA: A HELICAL RNA-STRUCTURE INCLUDING A TETRALOOP
ComponentsRNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*CP*CP*GP*CP*C P*UP*GP*G)-3')
KeywordsRNA / SINGLE STRAND / TETRALOOP / HAIRPIN / MISMATCHED
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsPerbandt, M. / Nolte, A. / Lorenz, S. / Erdmann, V.A. / Betzel, C.
CitationJournal: FEBS Lett. / Year: 1998
Title: Crystal structure of domain E of Thermus flavus 5S rRNA: a helical RNA structure including a hairpin loop.
Authors: Perbandt, M. / Nolte, A. / Lorenz, S. / Bald, R. / Betzel, C. / Erdmann, V.A.
History
DepositionNov 10, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,9702
Polymers12,9702
Non-polymers00
Water3,981221
1
A: RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*CP*CP*GP*CP*C P*UP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,4851
Polymers6,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*CP*CP*GP*CP*C P*UP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,4851
Polymers6,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.680, 42.680, 161.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: RNA chain RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*CP*CP*GP*CP*C P*UP*GP*G)-3') / DOMAIN E OF THERMUS FLAVUS 5S RRNA


Mass: 6484.910 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3.2 Å3/Da / Density % sol: 54 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 4-50 ℃ / Method: vapor diffusion
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
Conc.: 0.5 mM / Common name: RNA

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 4702 / % possible obs: 93.6 % / Observed criterion σ(I): 3 / Redundancy: 2.25 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 8.75
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.86 / Rsym value: 0.448 / % possible all: 96
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / % possible obs: 93.6 %
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 96 % / Redundancy: 1.87 % / Mean I/σ(I) obs: 1.86

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: 16NT FRAGMENT OF DOMAINA FROM 5SRNA

16nt


Resolution: 3→15 Å / Rfactor Rfree error: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.318 183 5 %RANDOM
Rwork0.241 ---
obs0.241 3667 97.1 %-
Displacement parametersBiso mean: 30.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 0 221 1079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.3 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.365 18 5 %
Rwork0.321 358 -
obs--96.2 %
Xplor fileSerial no: 1 / Param file: DNA-RNA.PARAM / Topol file: DNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 15 Å / Num. reflection obs: 2990 / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
LS refinement shell
*PLUS
Rfactor obs: 0.321

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