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- PDB-1nt8: Structural Characterisation of the Holliday junction formed by th... -

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Basic information

Entry
Database: PDB / ID: 1nt8
TitleStructural Characterisation of the Holliday junction formed by the sequence CCGGTACCGG at 2.00 A
Components5'-d(CpCpGpGpTpApCpCpGpG)-3'
KeywordsDNA / Holliday Junction / Calcium ion
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Model detailsThe structure is the more symmetrical form of the Holliday Junction with two calcium ions present
AuthorsCardin, C.J. / Gale, B.C. / Thorpe, J.H. / Texieira, S.C.M. / Gan, Y. / Moraes, M.I.A.A. / Brogden, A.L.
CitationJournal: To be Published
Title: Structural Analysis of two Holliday Junctions formed by the sequences TCGGTACCGA and CCGGTACCGG
Authors: Cardin, C.J. / Gale, B.C. / Thorpe, J.H. / Texieira, S.C.M. / Gan, Y. / Moraes, M.I.A.A. / Brogden, A.L.
History
DepositionJan 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: 5'-d(CpCpGpGpTpApCpCpGpG)-3'
B: 5'-d(CpCpGpGpTpApCpCpGpG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1724
Polymers6,0922
Non-polymers802
Water66737
1
A: 5'-d(CpCpGpGpTpApCpCpGpG)-3'
B: 5'-d(CpCpGpGpTpApCpCpGpG)-3'
hetero molecules

A: 5'-d(CpCpGpGpTpApCpCpGpG)-3'
B: 5'-d(CpCpGpGpTpApCpCpGpG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3448
Polymers12,1844
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)65.949, 23.756, 37.204
Angle α, β, γ (deg.)90.00, 109.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-110-

HOH

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Components

#1: DNA chain 5'-d(CpCpGpGpTpApCpCpGpG)-3'


Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, Calcium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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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 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.91→34.92 Å / Num. all: 6058 / Num. obs: 4276 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 34.53 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.106 / Net I/σ(I): 4.18
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 0.8 / Num. unique all: 624 / Rsym value: 0.849 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.92 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.868 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.253 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28262 167 4.5 %RANDOM
Rwork0.24659 ---
obs0.24834 3539 97.37 %-
all-4940 --
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: 34.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å2-0.77 Å2
2--2.84 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 2→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 2 37 443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021452
X-RAY DIFFRACTIONr_bond_other_d0.0020.02186
X-RAY DIFFRACTIONr_angle_refined_deg3.7683694
X-RAY DIFFRACTIONr_angle_other_deg1.7793472
X-RAY DIFFRACTIONr_chiral_restr0.1170.260
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02210
X-RAY DIFFRACTIONr_gen_planes_other00.022
X-RAY DIFFRACTIONr_nbd_refined0.170.251
X-RAY DIFFRACTIONr_nbd_other0.2270.2194
X-RAY DIFFRACTIONr_nbtor_other0.1170.2109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2820.222
X-RAY DIFFRACTIONr_metal_ion_refined0.0430.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3780.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.210
X-RAY DIFFRACTIONr_scbond_it3.6133452
X-RAY DIFFRACTIONr_scangle_it4.774.5694
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.207 9
Rwork0.233 248

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