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PDB | 3GCA | The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain

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Internal ID
64025
PDB Entry ID
3GCA
Title
The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain
Authors
Spitale, R.C.,Wedekind, J.E.
Primary Citation
AuthorsSpitale, R.C., Torelli, A.T., Krucinska, J., Bandarian, V., Wedekind, J.E.
TitleThe Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain.
JournalJ.Biol.Chem., v.284, pp.11012 - 11016, 2009
AbstractView
Pubmed19261617
DOI10.1074/jbc.C900024200
 
History
Deposition: 2009-02-21Release: 2009-03-03Last Modified: 2009-05-05
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
2.75n/a0.2450.272P 63 2 2
Unit Cell
Length [Å]a110.50b110.50c59.31
Angles [°]alpha90.00beta90.00gamma120.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1PreQ1 riboswitchA
Functional Class
RNA
Related PDB Entries
IDDetails
3GCA
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
PQ02-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILEC7H5N5O[View][View]
SO4SULFATE IONO4S2[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordRNA
TextPreQ1, PreQ0, riboswitch, RNA, ribosomal binding site, amptamer, metabolite
 
Polymeric Molecules
Chain A
DescriptionPreQ1 riboswitch
Polymer typepolyribonucleotide
Formula Weight10599.5
Source Methodsynthetic
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aApolyribonucleotiden/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
PQ02-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILEC7H5N5O175.149View
SO4SULFATE IONO4S296.058View
Crystallization Experiments
MethodVAPOR DIFFUSION, HANGING DROP
PH6.0
Temperature293.0
Details1.8 M Li2SO4, 0.10 M Na-cacodylate pH 6.0, 0.01 M Mg(SO4)2-, 5% (v/v) 1,3-propanediol and 2 mM spermine., VAPOR DIFFUSION, HANGING DROP, temperature 293K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
110.50110.5059.31
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.00120.00
Space Group
P 63 2 2
Diffraction Detector
DetectorCCD
TypeQuantum 315 CCD detector
DetailsVertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).
Collection Date2009-01-29
 
Diffraction Radiation
Monochromatorn/a
Diffraction ProtocolMAD
Wavelengthn/a
Wavelength List1.1395, 1.1407, 0.97622, 1.1395
 
Diffraction Source
SourceSYNCHROTRON
TypeSSRL BEAMLINE BL7-1
SiteSSRL
BeamlineBL7-1
 
Reflection Details
Observed Criterion Sigma (F)0.0
Observed Criterion Sigma (I)-3.0
Resolution (High)2.75
Resolution (Low)50.00
Number Reflections (All) n/a
Number Reflections (Observed)5990
Percent Possible (Observed)97.6
R Merge I (Observed)n/a
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plot75.0
Redundancy16.6
 
High Resolution Shell Details
Resolution(High)2.75
Resolution(Low)2.85
Percent Possible(All) 98.50
R Merge I(Observed)n/a
Mean I Over Sigma(Observed)6.5
R Sym I(Observed)0.360
Redundancy15.8
Num Unique Reflections(All)579
 
Refinement Statistics
Structure Solution MethodMAD
Resolution (High)2.75
Resolution (Low)28.33
Cut-off Sigma (F)0.0
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)5990
Number of Reflections (R-Free) 441
Percent Reflections (Observed)93.40
R-Factor (All)n/a
R-Factor (Observed)n/a
R-Work0.245
R-Free0.272
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal ModelRESTRAINED
Mean Isotropic B Value76.000
Anisotropic B[1][1]-21.00
Anisotropic B[1][2]n/a
Anisotropic B[1][3]n/a
Anisotropic B[2][2]-21.00
Anisotropic B[2][3]n/a
Anisotropic B[3][3]42.00
 
Resolution Shells
Shell Resol (High)2.75
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)65
Number of Reflections (R-Work)728
R-Factor (R-Work)0.438
R-Factor (R-Free)0.487
R-Free Error0.060
Percent Reflections (Observed)83.00
 
RMS Deviations
Parameter TypeDeviation From Ideal
c_improper_angle_d1.99
c_dihedral_angle_d20.3
c_angle_deg1.5
c_bond_d0.008
Coordinate Error
Luzzati ESD (Observed)0.44
Luzzati Sigma A (Observed)0.52
Luzzati Resolution Cutoff (Low)5.0
Luzzati ESD (R-Free Set)0.49
Luzzati Sigma A (R-Free Set)0.53
 
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms0
Nucleic Acid Atoms702
Heterogen Atoms23
Solvent Atoms0
 
Programs
Data CollectionHKL-2000
Data Reduction (intensity integration)DENZO
Data Reduction (data scaling)SCALEPACK
Structure SolutionPHENIX
Structure RefinementCNS 1.2
 
Software
Classificationdata collection
Software NameHKL-2000
 
Classificationmodel building
Software NamePHENIX
 
Classificationrefinement
Software NameCNS
Software Version 1.2
 
Sequence Chain
A
Sequence
 1   CUGGGUCGCA  GUAACCCCAG  UUAACAAAAC  AAG