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- PDB-1qc0: CRYSTAL STRUCTURE OF A 19 BASE PAIR COPY CONTROL RELATED RNA DUPLEX -

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Basic information

Entry
Database: PDB / ID: 1qc0
TitleCRYSTAL STRUCTURE OF A 19 BASE PAIR COPY CONTROL RELATED RNA DUPLEX
Components
  • 5'-R(*GP*CP*AP*CP*CP*GP*CP*UP*AP*CP*CP*AP*AP*CP*GP*GP*UP*GP*C)-3'
  • 5'-R(*GP*CP*AP*CP*CP*GP*UP*UP*GP*GP*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'
  • 5'-R(*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'
  • 5'-R(GP*CP*AP*CP*CP*GP*CP*UP*AP*C)-3'
KeywordsRNA / A-RNA STRUCTURE / RIBONUCLEIC ACID
Function / homologyAMMONIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 17, 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 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 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 1.5Apr 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(*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'
B: 5'-R(GP*CP*AP*CP*CP*GP*CP*UP*AP*C)-3'
C: 5'-R(*GP*CP*AP*CP*CP*GP*UP*UP*GP*GP*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'
D: 5'-R(*GP*CP*AP*CP*CP*GP*CP*UP*AP*CP*CP*AP*AP*CP*GP*GP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,32711
Polymers18,2014
Non-polymers1267
Water4,522251
1
A: 5'-R(*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'
B: 5'-R(GP*CP*AP*CP*CP*GP*CP*UP*AP*C)-3'
hetero molecules

A: 5'-R(*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'
B: 5'-R(GP*CP*AP*CP*CP*GP*CP*UP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,15610
Polymers12,0474
Non-polymers1086
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2
C: 5'-R(*GP*CP*AP*CP*CP*GP*UP*UP*GP*GP*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'
D: 5'-R(*GP*CP*AP*CP*CP*GP*CP*UP*AP*CP*CP*AP*AP*CP*GP*GP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2506
Polymers12,1772
Non-polymers724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.682, 43.682, 447.021
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

NH4

21B-202-

NH4

31B-204-

NH4

41C-203-

NH4

51C-206-

NH4

61D-205-

NH4

71D-207-

NH4

81A-208-

HOH

91A-391-

HOH

101B-209-

HOH

111B-210-

HOH

121B-213-

HOH

131B-267-

HOH

141B-272-

HOH

151B-290-

HOH

161B-392-

HOH

171C-286-

HOH

181C-363-

HOH

191C-399-

HOH

201D-269-

HOH

211D-292-

HOH

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Components

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RNA chain , 4 types, 4 molecules ABCD

#1: RNA chain 5'-R(*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'


Mass: 2887.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN E. COLI.
#2: RNA chain 5'-R(GP*CP*AP*CP*CP*GP*CP*UP*AP*C)-3'


Mass: 3135.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN E. COLI.
#3: RNA chain 5'-R(*GP*CP*AP*CP*CP*GP*UP*UP*GP*GP*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'


Mass: 6125.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN E. COLI.
#4: RNA chain 5'-R(*GP*CP*AP*CP*CP*GP*CP*UP*AP*CP*CP*AP*AP*CP*GP*GP*UP*GP*C)-3'


Mass: 6051.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN E. COLI.

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Non-polymers , 2 types, 258 molecules

#5: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAINS A AND B FORM A 9.5 BASE PAIR DUPLEX; A CRYSTALLOGRAPHIC TWO-FOLD AXIS GENERATES THE ...CHAINS A AND B FORM A 9.5 BASE PAIR DUPLEX; A CRYSTALLOGRAPHIC TWO-FOLD AXIS GENERATES THE REMAINING 9.5 BASE PAIRS OF THIS DUPLEX.

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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: 2.3 Å3/Da / Density % sol: 54 %
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 F110.9188
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 15, 1997
RIGAKU RAXIS2IMAGE PLATEMay 30, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91881
21.54181
ReflectionResolution: 1.55→40 Å / Num. all: 24898 / Num. obs: 22779 / % possible obs: 91.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.9
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.7 / % possible all: 94.8
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
SOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A-RNA

Resolution: 1.55→40 Å / Num. parameters: 13059 / Num. restraintsaints: 16977 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0
Stereochemistry target values: PARKINSON, VOJTECHOVSKY, CLOWNEY, BRUNGER & BERMAN, ACTA CRYST D52, 57-64 (1996)
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.6%
RfactorNum. reflection% reflection
Rfree0.2144 1144 5 %
Rwork0.1498 --
all0.1533 22779 -
obs0.1533 18563 91.5 %
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91, 201-228 (1973)
Refine analyzeOccupancy sum hydrogen: 561 / Occupancy sum non hydrogen: 1383
Refinement stepCycle: LAST / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1767 7 251 2025
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.015
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.077
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_plane_restr0.015
LS refinement shell
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 1.61 Å / Rfactor Rfree: 0.288 / Rfactor obs: 0.261

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