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- PDB-467d: The structure of a decamer forming a four-way junction -

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Basic information

Entry
Database: PDB / ID: 467d
TitleThe structure of a decamer forming a four-way junction
ComponentsDNA (5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3')
KeywordsDNA / G:A MISMATCHES / FOUR-WAY-JUNCTION
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MAD, MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsOrtiz-Lombardia, M. / Coll, M.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of a DNA Holliday junction
Authors: Ortiz-Lombardia, M. / Gonzalez, A. / Eritja, R. / Aymami, J. / Azorin, F. / Coll, M.
History
DepositionApr 22, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,1422
Polymers6,1422
Non-polymers00
Water54030
1
A: DNA (5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3')

A: DNA (5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,2844
Polymers12,2844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)64.200, 23.740, 38.300
Angle α, β, γ (deg.)90.00, 112.43, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

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Components

#1: DNA chain DNA (5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3')


Mass: 3071.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 6.7% MPD, 0.2M MGCL2, 1.0MM DNA DECAMER AGAINST 45% MPD IN DEPOSIT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MGCL211
3MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mMDNA1drop
210 %MPD1drop
30.2 M1dropMgCl2
445 %MPD1reservoir0.5ml

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.16→19.39 Å / Num. all: 2786 / Num. obs: 2786 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.4
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 5.2 / % possible all: 75.5
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 75.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
AMoREphasing
REFMACrefinement
CCP4phasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 2.16→19.39 Å / Cross valid method: THROUGHOUT / σ(F): -3
RfactorNum. reflection% reflectionSelection details
Rfree0.288 260 10 %RANDOM
Rwork0.24 ---
all0.257 2526 --
obs0.257 2526 92 %-
Refinement stepCycle: LAST / Resolution: 2.16→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 0 30 438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): -3 / % reflection Rfree: 10 % / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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