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- PDB-1p4y: Effect of Sequence on the Conformational Geometry of DNA Holliday... -

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Basic information

Entry
Database: PDB / ID: 1p4y
TitleEffect of Sequence on the Conformational Geometry of DNA Holliday Junctions
Components5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
KeywordsDNA / Holliday Junction / DNA Four-Way Junction
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHays, F.A. / Vargason, J.M. / Ho, P.S.
CitationJournal: Biochemistry / Year: 2003
Title: Effect of Sequence on the Conformation of DNA Holliday Junctions
Authors: Hays, F.A. / Vargason, J.M. / Ho, P.S.
History
DepositionApr 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
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'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1866
Polymers6,0942
Non-polymers924
Water1,946108
1
A: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
hetero molecules

A: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,37212
Polymers12,1884
Non-polymers1848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)66.513, 24.179, 37.004
Angle α, β, γ (deg.)90.0, 110.010, 90.0
Int Tables number5
Space group name H-MC121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHAINS A AND B. THE FULL FOUR STRANDED HOLLIDAY JUNCTION STRUCTURE CAN BE GENERATED BY THE FOLLOWING: matrix= ( -1.00000 -0.00046 -0.00015 ) ( -0.00046 1.00000 0.00072 ) ( 0.00015 0.00072 -1.00000 ) translation= (-12.65734 -0.02663 34.77174)

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Components

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


Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC ...Details: DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.94 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 298 K / pH: 7
Details: 0.5mM DNA, 25mM sodium cacodylate, 7.5mM CaCl2, 0.1mM SPERMINE TETRAHYDROCHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2CaCl211
3SPERMINE TETRAHYDROCHLORIDE11
4H2O11
5sodium cacodylate12
6CaCl212
7SPERMINE TETRAHYDROCHLORIDE12
8H2O12
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.5 mMDNA1drop
225 mMsodium cacodylate1droppH7.0
37.5 mM1dropCaCl2
40.1 mMspermine tetrahydrochloride1drop
528 %(v/v)MPD1reservoir
61
71
81

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2003
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.65→22.55 Å / Num. obs: 4940 / % possible obs: 74 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 1.6 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.14 / % possible all: 21.7
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Num. obs: 5137 / % possible obs: 78.7 % / Rmerge(I) obs: 0.049 / Num. measured all: 50581
Reflection shell
*PLUS
% possible obs: 48 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UD0008

Resolution: 1.7→22.5 Å / Rfactor Rfree error: 0.012 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 490 10 %RANDOM
Rwork0.229 ---
obs0.229 4436 77.1 %-
all-4940 --
Displacement parametersBiso mean: 8.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.7→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 4 108 516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 39 9.4 %
Rwork0.209 374 -
obs--40.8 %
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.57

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