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- PDB-3hqe: Crystal Structure of the decamer CGGGCGCCCG forming a Holliday ju... -

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Basic information

Entry
Database: PDB / ID: 3hqe
TitleCrystal Structure of the decamer CGGGCGCCCG forming a Holliday junction
Components5'-D(*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3'
KeywordsDNA / Four-way junction with B-DNA arms
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Gautham, N.
CitationJournal: To be Published
Title: Sequence dependent structural variation of Holliday junction - crystal structure of d(CGGGCGCCCG)4
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionJun 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0942
Polymers6,0942
Non-polymers00
Water18010
1
A: 5'-D(*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3'
B: 5'-D(*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3'

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


Theoretical massNumber of molelcules
Total (without water)12,1884
Polymers12,1884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2790 Å2
ΔGint-11 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.004, 22.813, 40.708
Angle α, β, γ (deg.)90.00, 116.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Drop contains 1mM DNA, 50mM buffer, 100mM MgCl2, 1mM spermine, 50% MPD in reservior , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 8, 2008 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 1271 / Num. obs: 1239 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 3.51 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.109 / Net I/σ(I): 2.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.54 % / Rmerge(I) obs: 0.4579 / Mean I/σ(I) obs: 1 / Num. unique all: 109 / Rsym value: 0.4162 / % possible all: 96.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1P4Y

1p4y


Resolution: 2.94→19.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.956 / SU B: 18.845 / SU ML: 0.321 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23946 56 5 %RANDOM
Rwork0.21517 ---
all0.2251 1129 --
obs0.2166 1073 93.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.104 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20.71 Å2
2---0.97 Å20 Å2
3---0.46 Å2
Refine analyzeLuzzati coordinate error obs: 0.493 Å
Refinement stepCycle: LAST / Resolution: 2.94→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 10 414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021452
X-RAY DIFFRACTIONr_angle_refined_deg3.1583694
X-RAY DIFFRACTIONr_chiral_restr0.1120.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02210
X-RAY DIFFRACTIONr_nbd_refined0.2740.2115
X-RAY DIFFRACTIONr_nbtor_refined0.350.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.29
X-RAY DIFFRACTIONr_scbond_it5.1153666
X-RAY DIFFRACTIONr_scangle_it4.3264.5694
LS refinement shellResolution: 2.942→3.017 Å / Rfactor Rfree error: 0.456 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.799 4 -
Rwork0.534 71 -
obs-71 97.4 %

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