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- PDB-1m6g: Structural Characterisation of the Holliday Junction TCGGTACCGA -

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Basic information

Entry
Database: PDB / ID: 1m6g
TitleStructural Characterisation of the Holliday Junction TCGGTACCGA
Components5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'
KeywordsDNA / Holliday Junction / Strontium derivative / Four-way junction
Function / homologySTRONTIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å
AuthorsThorpe, J.H. / Gale, B.C. / Teixeira, S.C.M. / Cardin, C.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4)
Authors: Thorpe, J.H. / Gale, B.C. / Teixeira, S.C.M. / Cardin, C.J.
History
DepositionJul 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _software.version
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 / 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_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: 5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'
B: 5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5287
Polymers6,0902
Non-polymers4385
Water1,928107
1
A: 5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'
B: 5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)13,05614
Polymers12,1804
Non-polymers87610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)64.302, 25.034, 36.778
Angle α, β, γ (deg.)90.00, 110.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SECTION OF HOLLIDAY JUNCTION
#2: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: cacodylate, strontium chloride, MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylateCacodylic acid11
2SrCl211
3MPD11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.649→34.503 Å / Num. obs: 6703 / Redundancy: 5.41 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.2957 / Rsym value: 0.082
Reflection shellResolution: 1.652→1.695 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.332 / Num. unique all: 408 / Rsym value: 0.148

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
SCALAdata scaling
XTALVIEWrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.652→34.503 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9 / SU B: 2.69 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29566 316 4.8 %RANDOM
Rwork0.21486 ---
all0.2185 ---
obs0.2148 6621 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å2-0.35 Å2
2--2.32 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.652→34.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 5 107 516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021452
X-RAY DIFFRACTIONr_bond_other_d0.0020.02192
X-RAY DIFFRACTIONr_angle_refined_deg2.8683694
X-RAY DIFFRACTIONr_angle_other_deg1.7143484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024
X-RAY DIFFRACTIONr_nbd_refined0.1470.252
X-RAY DIFFRACTIONr_nbd_other0.2130.2194
X-RAY DIFFRACTIONr_nbtor_other0.1090.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0480.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3390.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it2.543452
X-RAY DIFFRACTIONr_scangle_it3.3084.5694
X-RAY DIFFRACTIONr_rigid_bond_restr1.7132452
X-RAY DIFFRACTIONr_sphericity_free4.622112
X-RAY DIFFRACTIONr_sphericity_bonded3.4352404
LS refinement shellResolution: 1.652→1.695 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 19
Rwork0.212 408

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