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- PDB-1qcu: CRYSTAL STRUCTURE OF AN 18 BASE PAIR COPY CONTROL RELATED RNA DUPLEX -

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Basic information

Entry
Database: PDB / ID: 1qcu
TitleCRYSTAL STRUCTURE OF AN 18 BASE PAIR COPY CONTROL RELATED RNA DUPLEX
Components
  • 5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'
  • 5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3'
KeywordsRNA / A-RNA STRUCTURE / RIBONUCLEIC ACID
Function / homologyAMMONIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKlosterman, P.S. / Shah, S.A. / Steitz, T.A.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structures of two plasmid copy control related RNA duplexes: An 18 base pair duplex at 1.20 A resolution and a 19 base pair duplex at 1.55 A resolution.
Authors: Klosterman, P.S. / Shah, S.A. / Steitz, T.A.
History
DepositionMay 14, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Nov 11, 1999Provider: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3'
B: 5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'
C: 5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'
D: 5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2018
Polymers14,1294
Non-polymers724
Water3,513195
1
A: 5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3'
B: 5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1376
Polymers7,0642
Non-polymers724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'
D: 5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,0642
Polymers7,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.806, 43.806, 29.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Cell settingtrigonal
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-202-

NH4

21A-203-

NH4

31B-201-

NH4

41B-204-

NH4

51A-206-

HOH

61A-207-

HOH

71B-205-

HOH

81B-208-

HOH

91B-332-

HOH

101B-352-

HOH

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Components

#1: RNA chain 5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3'


Mass: 3752.306 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain 5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'


Mass: 3312.042 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CRYSTALS EXHIBIT 36-FOLD STATIC DISORDER, SUCH THAT THERE IS ONE CONFORMATION OF THE SUGAR- ...THE CRYSTALS EXHIBIT 36-FOLD STATIC DISORDER, SUCH THAT THERE IS ONE CONFORMATION OF THE SUGAR-PHOSPHATE BACKBONE BUT THE BASE COMPOSITION IS AVERAGED AT EACH POSITION. THE CRYSTALS WERE GROWN FROM TWO 18MER OLIGORIBONUCLEOTIDES, WITH SEQUENCES 5'-R(*CP*AP*CP*CP*GP*UP*UP*GP*GP*UP*AP*GP* CP*GP*GP*UP*GP*C)-3' AND 5'-R(*CP*AP*CP*CP*GP*CP*UP*AP*CP* CP*AP*AP*CP*GP*GP*UP*GP*C)-3' RESPECTIVELY. THESE SEQUENCES OCCUR NATURALLY IN E. COLI. THE AVERAGING PRODUCES CRYSTALS WITH ONE TURN, 11 BASE PAIRS, OF A RNA IN THE ASYMMETRIC UNIT. THIS IS MODELED USING ONE G AND ONE C RESIDUE CONNECTED TO EACH RIBOSE C1*, WITH PARTIAL OCCUPANCIES EQUAL TO THE FREQUENCIES OF PURINES AND PYRIMIDINES, RESPECTIVELY, IN THE 18MER DUPLEX. STRAND A, ALL G'S, AND STRAND C, ALL C'S, HAVE IDENTICAL RIBOSE AND PHOSPHATE COORDINATES AND ATOMIC DISPLACEMENT PARAMETERS; LIKEWISE STRAND B, ALL C'S, AND STRAND D, ALL G'S, HAVE IDENTICAL SUGAR - PHOSPHATE BACKBONES.

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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: 2.4 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: (NH4)2SO4, SODIUM CACODYLATE, MGCL2, ROP PROTEIN, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2SODIUM CACODYLATE11
3MGCL211
4ROP PROTEIN11
5(NH4)2SO412
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 mMRNA oligo1drop
21.0 mMrop protein1drop
31.05 Mammonium sulfate1drop
45 mMsodium cacodylate1drop
51 mM1dropMgCl2
60.02 %sodium azide1drop
72.1 Mammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONCHESS A110.914
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDate
PRINCETON 2K1CCDMay 17, 1997
RIGAKU RAXIS2IMAGE PLATEJul 6, 1997
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9141
21.54181
ReflectionResolution: 1.2→30 Å / Num. all: 19666 / Num. obs: 18266 / % possible obs: 92.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 31.8
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.2 / % possible all: 77.1
Reflection
*PLUS
% possible obs: 93 %
Reflection shell
*PLUS
% possible obs: 77 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A-RNA

Resolution: 1.2→30 Å / Num. parameters: 7977 / Num. restraintsaints: 21649 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0
StereochEM target val spec case: USED THE AVERAGE OF GUA C6 O6, ADE C6 N6 BOND LENGTHS AS THE C6 O6 BOND LENGTH
Stereochemistry target values: Parkinson et al.
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 6.5% THE MOLECULE CRYSTALLIZED IN SPACE GROUP P321. HOWEVER THE REFINEMENT WAS CARRIED OUT IN THE LOWER SPACE GROUP P3. THE COORDINATES ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 6.5% THE MOLECULE CRYSTALLIZED IN SPACE GROUP P321. HOWEVER THE REFINEMENT WAS CARRIED OUT IN THE LOWER SPACE GROUP P3. THE COORDINATES DEPOSITED ARE FOR THE SPACE GROUP P3.
RfactorNum. reflection% reflection
Rfree0.1503 909 5 %
all0.1175 18266 -
obs0.1158 -92.5 %
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL., 91 201-228 (1973)
Refine analyzeNum. disordered residues: 22 / Occupancy sum hydrogen: 227 / Occupancy sum non hydrogen: 578
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1415 4 195 1614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.029
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.026
X-RAY DIFFRACTIONs_approx_iso_adps0.086
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.202 / Rfactor obs: 0.116 / Rfactor Rfree: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.93

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