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- PDB-1mhk: Crystal Structure Analysis of a 26mer RNA molecule, representing ... -

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Basic information

Entry
Database: PDB / ID: 1mhk
TitleCrystal Structure Analysis of a 26mer RNA molecule, representing a new RNA motif, the hook-turn
Components
  • RNA 12-mer BCh12
  • RNA 14-mer BCh12
KeywordsRNA / helix / 180 degree turn
Function / homologyBROMIDE ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSzep, S. / Wang, J. / Moore, P.B.
CitationJournal: RNA / Year: 2003
Title: The crystal structure of a 26-nucleotide RNA containing a hook-turn
Authors: Szep, S. / Wang, J. / Moore, P.B.
History
DepositionAug 20, 2002Deposition site: NDB / Processing site: RCSB
Revision 1.0Sep 6, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
S: RNA 12-mer BCh12
L: RNA 14-mer BCh12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3703
Polymers8,2902
Non-polymers801
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.169, 62.510, 50.933
Angle α, β, γ (deg.)90.00, 98.76, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11S-16-

HOH

21L-19-

HOH

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Components

#1: RNA chain RNA 12-mer BCh12


Mass: 3810.352 Da / Num. of mol.: 1 / Fragment: fragment of 5S rRNA Loop E / Source method: obtained synthetically
Details: 5S rRNA Loop E region, sequence from Chromatium minutissimum
#2: RNA chain RNA 14-mer BCh12


Mass: 4479.691 Da / Num. of mol.: 1 / Fragment: fragment of 5S rRNA Loop E / Source method: obtained synthetically
Details: 5S rRNA Loop E region, sequence from Chromatium minutissimum
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, magnesium chloride, spermidine, tris-hydrogen chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP at 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2MgCl211
3spermidine11
4tris-HCl11
5(NH4)2SO412
6MgCl212
7tris-HCl12
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaDetails
11.8 Mammonium sulfate1
25 mM1MgCl2
31 mM1
450 mMTris-HCl1pH7.5
51
61
71

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11931
21931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X2520.91939
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEJan 31, 2001focusing mirrors
CUSTOM-MADE2CCDApr 13, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1focusing mirrorsSINGLE WAVELENGTHMx-ray1
2double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.919391
ReflectionResolution: 2.5→15 Å / Num. obs: 3220 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 17.69 % / Biso Wilson estimate: 57.5 Å2 / Rsym value: 0.128 / Net I/σ(I): 10.35
Reflection shellHighest resolution: 2.5 Å / Redundancy: 4.59 % / Mean I/σ(I) obs: 2.55 / Num. unique all: 307 / Rsym value: 0.342 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 3175 / Num. measured all: 56979 / Rmerge(I) obs: 0.128
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.342

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6mer A-form RNA helix

6mer


Resolution: 2.5→15 Å / Rfactor Rfree error: 0.017 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: CNS standard parameter files:dna_rnarep.param
RfactorNum. reflection% reflectionSelection details
Rfree0.27 252 8.4 %RANDOM
Rwork0.2391 ---
obs0.243 3011 93.6 %-
all-3217 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.1757 Å2 / ksol: 0.402743 e/Å3
Displacement parametersBiso mean: 55.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.17 Å20 Å220.29 Å2
2--5.29 Å20 Å2
3----11.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 548 1 21 570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.08
X-RAY DIFFRACTIONc_dihedral_angle_d14
X-RAY DIFFRACTIONc_improper_angle_d1.46
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 31 7.4 %
Rwork0.404 359 -
obs--78.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA_REP-BR2.PARAMDNA-RNA-BR2.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.46

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