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- PDB-3iqr: SAM-I riboswitch from T. tencongensis variant A94G bound with SAM -

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Basic information

Entry
Database: PDB / ID: 3iqr
TitleSAM-I riboswitch from T. tencongensis variant A94G bound with SAM
ComponentsSAM-I riboswitch
KeywordsRNA / riboswitch / SAM / kink-turn / psuedoknot
Function / homology: / S-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsMontange, R.K. / Batey, R.T.
CitationJournal: Structure / Year: 2010
Title: Free state conformational sampling of the SAM-I riboswitch aptamer domain.
Authors: Stoddard, C.D. / Montange, R.K. / Hennelly, S.P. / Rambo, R.P. / Sanbonmatsu, K.Y. / Batey, R.T.
History
DepositionAug 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM-I riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,20411
Polymers30,5691
Non-polymers1,63410
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SAM-I riboswitch
hetero molecules

A: SAM-I riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,40722
Polymers61,1392
Non-polymers3,26920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5340 Å2
ΔGint-47 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.804, 61.804, 157.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain SAM-I riboswitch


Mass: 30569.322 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 303 K / Method: hanging drop / pH: 7 / Details: pH 7.0, hanging drop, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 4, 2006
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. all: 18976 / Num. obs: 18805 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.98 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.4
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 4.81 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GIS
Resolution: 2.55→19.93 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.293 1814 9.6 %
Rwork0.249 --
obs0.249 18805 98.9 %
all-18976 -
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.32 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 56.66 Å2
Baniso -1Baniso -2Baniso -3
1-11.52 Å20 Å20 Å2
2--11.52 Å20 Å2
3----23.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.55→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2030 36 48 2114
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.5
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it1.432
X-RAY DIFFRACTIONc_scangle_it2.212.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.426 291 9.2 %
Rwork0.408 2864 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramdna-rna_rep_revise.top
X-RAY DIFFRACTION2ion2.paramion2.top
X-RAY DIFFRACTION3dna-rna_rep_revise.paramwater.top
X-RAY DIFFRACTION4sam3.paramsam3.top

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