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- PDB-1p54: Effect of Sequence on the Conformational Geometry of DNA Holliday... -

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Basic information

Entry
Database: PDB / ID: 1p54
TitleEffect of Sequence on the Conformational Geometry of DNA Holliday Junctions
Components5'-D(*CP*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G)-3'
KeywordsDNA / DNA Holliday Junction / Four-Way Junction / stacked-X junction / brominated uracil
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 25, 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 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry / _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: 5'-D(*CP*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G)-3'
B: 5'-D(*CP*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2834
Polymers6,2202
Non-polymers632
Water1,56787
1
A: 5'-D(*CP*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G)-3'
B: 5'-D(*CP*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)12,5668
Polymers12,4394
Non-polymers1264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)64.840, 22.580, 38.070
Angle α, β, γ (deg.)90.00, 106.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-37-

NA

21A-68-

HOH

31A-86-

HOH

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 0.00001 0.00000) (0.00001 1.00000 -0.00002) (0.00000 -0.00002 -1.00000) translation = (0.00022 0.00018 -0.00034)

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Components

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


Mass: 3109.874 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.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.93 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 0.6mM DNA, 5mM Tris-HCL, 120mM calcium acetate, 16% 2-methyl-2,4-pentane diol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HCL11
2calcium acetate11
32-methyl-2,4-pentane diol11
4H2O11
5calcium acetate12
6Tris-HCL12
72-methyl-2,4-pentane diol12
8H2O12
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.6 mMDNA1drop
25 mMTris-HCl1droppH7.5
3120 mMcalcium acetate1drop
416 %MPD1drop
520 %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: Dec 19, 2002
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.8→19.18 Å / Num. obs: 4177 / % possible obs: 82 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 4.3 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 4.05
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.189 / % possible all: 34.9
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / Num. obs: 4011 / Num. measured all: 13013
Reflection shell
*PLUS
% possible obs: 34.9 % / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L6B USED FOR INITIAL SOLUTION VIA MOLECULAR REPLACEMENT

1l6b


Resolution: 1.9→19.18 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 388 10.4 %RANDOM
Rwork0.215 ---
obs0.215 3745 86.7 %-
all-4011 --
Displacement parametersBiso mean: 9.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 2 87 493
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg0.9
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_d1.37
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: 1.9→2.02 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 37 8.8 %
Rwork0.259 385 -
obs--60.1 %
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.88
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.37

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