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- PDB-1p4z: Effect of Sequence on the Conformational Geometry of DNA Holliday... -

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Basic information

Entry
Database: PDB / ID: 1p4z
TitleEffect of Sequence on the Conformational Geometry of DNA Holliday Junctions
Components5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3'
KeywordsDNA / B-DNA / Double Helix
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Nov 16, 2011Group: Atomic model
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,1144
Polymers3,0451
Non-polymers693
Water1,15364
1
A: 5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,2288
Polymers6,0902
Non-polymers1386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Unit cell
Length a, b, c (Å)33.380, 33.380, 87.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-11-

HOH

21A-32-

HOH

31A-33-

HOH

41A-43-

HOH

51A-62-

HOH

DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE CHAIN. GENERATION OF THE DOUBLE HELIX CAN BE PERFORMED WITH THE FOLLOWING: matrix= (0.50000 0.86603 0.00000 ) (0.86603 -0.50000 0.00000 ) (0.00000 0.00000 -1.00000 ) translation= (16.68855 -28.90537 14.61163)

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Components

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


Mass: 3045.004 Da / Num. of mol.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.87 Å3/Da / Density % sol: 33.78 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.6mM DNA, 5mM TRIS(HCl), 25mM Ca-Acetate, 7% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.50
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS(HCl)11
2Ca-Acetate11
3MPD11
4H2O11
5Ca-Acetate12
6MPD12
7TRIS(HCl)12
8H2O12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.6 mMDNA1drop
25 mMTris-HCl1droppH7.5
325 mMcalcium acetate1drop
47 %MPD1drop
530 %MPD1reservoir
61
71
81

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2002 / Details: BENT CONICAL SI-MIRROR (RH COATING)
RadiationMonochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→17.47 Å / Num. obs: 2143 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 3.6 Å2 / Rmerge(I) obs: 0.039
Reflection shellResolution: 2→2.13 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 2.38 / % possible all: 74.6
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. obs: 2143 / % possible obs: 94.6 % / Rmerge(I) obs: 0.048 / Num. measured all: 32690
Reflection shell
*PLUS
% possible obs: 53.2 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED RESULTS OF STRUCTURE WITH ISOMORPHOUS UNIT CELL DIMENSIONS

Resolution: 2→17.47 Å / Rfactor Rfree error: 0.019 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 195 9.1 %RANDOM
Rwork0.236 ---
obs0.236 2143 95.1 %-
all-2143 --
Displacement parametersBiso mean: 7.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→17.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 3 64 269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.23
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: 2→2.13 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 21 7.9 %
Rwork0.242 244 -
obs--74.6 %
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.75
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.23

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