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- PDB-1dcw: STRUCTURE OF A FOUR-WAY JUNCTION IN AN INVERTED REPEAT SEQUENCE. -

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Basic information

Entry
Database: PDB / ID: 1dcw
TitleSTRUCTURE OF A FOUR-WAY JUNCTION IN AN INVERTED REPEAT SEQUENCE.
ComponentsDNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
KeywordsDNA / HOLLIDAY JUNCTION / INVERTED REPEAT / FOUR-WAY JUNCTION / DEOXYRIBONUCLEIC ACID
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsEichman, B.F. / Vargason, J.M. / Mooers, B.H.M. / Ho, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions.
Authors: Eichman, B.F. / Vargason, J.M. / Mooers, B.H. / Ho, P.S.
History
DepositionNov 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,2075
Polymers12,1844
Non-polymers231
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.500, 23.500, 76.900
Angle α, β, γ (deg.)90.00, 114.80, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-38-

HOH

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Components

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


Mass: 3045.992 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growpH: 7 / Details: MPD, CACL2, SODIUM CACODYLATE, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1CACL211
2SODIUM CACODYLATE11
3MPD11
4MPD12
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
10.25 mMDNA1
275 mMsodium cacodylate1
315 mM1CaCl2
42.5 %11
530 %(v/v)MPD12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→30.16 Å / Num. obs: 6322 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.7 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 18370
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→8 Å / Cross valid method: THROUGHOUT / σ(F): 3
Details: ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS
RfactorNum. reflection% reflectionSelection details
Rfree0.317 598 10 %RANDOM
Rwork0.23 ---
obs0.23 5723 88.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.5841 Å20 Å2-1.8465 Å2
2--16.8867 Å20 Å2
3----8.3025 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 1 91 900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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: 2.1→2.19 Å / Total num. of bins used: 8 /
Num. reflection% reflection
Rfree55 -
Rwork450 -
obs-68 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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