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- PDB-1br3: CRYSTAL STRUCTURE OF AN 82-NUCLEOTIDE RNA-DNA COMPLEX FORMED BY T... -

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Basic information

Entry
Database: PDB / ID: 1br3
TitleCRYSTAL STRUCTURE OF AN 82-NUCLEOTIDE RNA-DNA COMPLEX FORMED BY THE 10-23 DNA ENZYME
Components
  • DNA (10-23 DNA ENZYME)
  • RNA (5'-R(*GP*GP*AP*CP*AP*GP*AP*UP*GP*GP*GP*AP*G)-3')
KeywordsDNA-RNA HYBRID / DNA ENZYME / RIBOZYME / HOLLIDAY JUNCTION / DNA/RNA HYBRID / DNA-RNA HYBRID complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsNowakowski, J. / Shim, P.J. / Prasad, G.S. / Stout, C.D. / Joyce, G.F.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme.
Authors: Nowakowski, J. / Shim, P.J. / Prasad, G.S. / Stout, C.D. / Joyce, G.F.
History
DepositionAug 13, 1998Processing site: NDB
Revision 1.0Feb 23, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*AP*CP*AP*GP*AP*UP*GP*GP*GP*AP*G)-3')
B: DNA (10-23 DNA ENZYME)


Theoretical massNumber of molelcules
Total (without water)12,8112
Polymers12,8112
Non-polymers00
Water0
1
A: RNA (5'-R(*GP*GP*AP*CP*AP*GP*AP*UP*GP*GP*GP*AP*G)-3')
B: DNA (10-23 DNA ENZYME)

A: RNA (5'-R(*GP*GP*AP*CP*AP*GP*AP*UP*GP*GP*GP*AP*G)-3')
B: DNA (10-23 DNA ENZYME)


Theoretical massNumber of molelcules
Total (without water)25,6224
Polymers25,6224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)63.450, 63.450, 216.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122

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Components

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


Mass: 4299.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA SUBSTRATE
#2: DNA chain DNA (10-23 DNA ENZYME)


Mass: 8511.482 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 4.77 Å3/Da / Density % sol: 74.23 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 24.5 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.4 mMprotein1drop
250 mMsodium cacodylate1reservoir
330 mM1reservoirMgCl2
41 mMspermine1reservoir
50.9 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorDetector: IMAGE PLATE / Date: Feb 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 5739 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 4.3 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.8 / % possible all: 98
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 98 % / Redundancy: 4 % / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
SOFTWAREAT SYNCHROTRONdata reduction
RefinementMethod to determine structure: MIR / Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 573 10 %RANDOM
Rwork0.227 ---
obs0.227 5739 98.2 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 850 0 0 850
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.24
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.54 84 10 %
Rwork0.48 588 -
Xplor fileSerial no: 1 / Param file: DNA-RNA-MULTI-END.PARAM / Topol file: TOP_NDBX3.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.54 / Rfactor Rwork: 0.48

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