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- PDB-1kxk: Crystal Structure of a RNA Molecule Containing Domain 5 and 6 of ... -

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Basic information

Entry
Database: PDB / ID: 1kxk
TitleCrystal Structure of a RNA Molecule Containing Domain 5 and 6 of the Yeast ai5g Group II Self-splicing Intron
Componentsai5g group II Self-splicing intron
KeywordsRNA / double helix / tetraloop / tetraloop receptor / two-nucleotide bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsZhang, L. / Doudna, J.A.
CitationJournal: Science / Year: 2002
Title: Structural insights into group II intron catalysis and branch-site selection.
Authors: Zhang, L. / Doudna, J.A.
History
DepositionJan 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: ai5g group II Self-splicing intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6693
Polymers22,6201
Non-polymers492
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.987, 90.987, 235.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain ai5g group II Self-splicing intron


Mass: 22620.477 Da / Num. of mol.: 1 / Fragment: domain 5 and 6 / Source method: obtained synthetically
Details: THE SEQUENCE IS FROM Saccharomyces cerevisiae (yeast). in vitro transcription.
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 6.23 Å3/Da / Density % sol: 80.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: HEPES-KOH, magnesium chloride, ammonium sulfate, spermine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES-KOH11
2MgCl11
3ammonium sulfate11
4spermine11
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15-6 mg/mlRNA1drop
22.5 mM1dropMgCl2
310 mMHEPES-KOH1droppH7.0
450 mMHEPES-KOH1reservoirpH7.0
510 mM1reservoirMgCl2
61-1.2 Mammonium sulfate1reservoir
70.1 mMspermine1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X2520.92, 0.9194, 0.9273, 0.9020
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 22, 2001
ADSC QUANTUM 42CCDApr 22, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) or (220)SINGLE WAVELENGTHMx-ray1
2Si(111) or (220)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.921
30.91941
40.92731
50.9021
ReflectionResolution: 3→30 Å / Num. all: 12289 / Num. obs: 10014 / % possible obs: 81.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.5 % / Rsym value: 0.054 / Net I/σ(I): 23.4
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.43 / % possible all: 51.7
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 85.8 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 51.7 % / Rmerge(I) obs: 0.43

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 3→30 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1031 -random
Rwork0.2476 ---
all0.2497 12289 --
obs0.2497 10014 81.5 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1497 2 0 1499
LS refinement shellResolution: 3→3.11 Å
RfactorNum. reflection% reflection
Rfree0.4421 46 -
Rwork0.4186 --
obs--51.3 %
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006591
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.15807
LS refinement shell
*PLUS
Rfactor obs: 0.4186

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