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- PDB-1nqs: Structural Characterisation of the Holliday Junction formed by th... -

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Basic information

Entry
Database: PDB / ID: 1nqs
TitleStructural Characterisation of the Holliday Junction formed by the sequence d(TCGGTACCGA) at 1.97 A
Components5'-d(TpCpGpGpTpApCpCpGpA)-3'
KeywordsDNA / Holliday Junction / Calcium ion
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
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 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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(TpCpGpGpTpApCpCpGpA)-3'
B: 5'-d(TpCpGpGpTpApCpCpGpA)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1303
Polymers6,0902
Non-polymers401
Water75742
1
A: 5'-d(TpCpGpGpTpApCpCpGpA)-3'
B: 5'-d(TpCpGpGpTpApCpCpGpA)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)12,2606
Polymers12,1804
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)65.588, 23.628, 37.223
Angle α, β, γ (deg.)90.00, 111.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-18-

HOH

21B-123-

HOH

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Components

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


Mass: 3045.005 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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, calcium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING 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 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.97→34.71 Å / Num. all: 3906 / Num. obs: 3877 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 39.038 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 6.1
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 6.1 / Num. unique all: 549 / Rsym value: 0.296 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→34.71 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27779 176 4.6 %RANDOM
Rwork0.22304 ---
obs0.22538 3691 99 %-
all-3728 --
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.038 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-1.12 Å2
2--2.94 Å20 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 1.97→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 1 42 447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021452
X-RAY DIFFRACTIONr_bond_other_d0.0030.02192
X-RAY DIFFRACTIONr_angle_refined_deg1.9823694
X-RAY DIFFRACTIONr_angle_other_deg1.6493484
X-RAY DIFFRACTIONr_chiral_restr0.0650.260
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024
X-RAY DIFFRACTIONr_nbd_refined0.1530.251
X-RAY DIFFRACTIONr_nbd_other0.210.2197
X-RAY DIFFRACTIONr_nbtor_other0.0890.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.228
X-RAY DIFFRACTIONr_metal_ion_refined0.070.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3390.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.215
X-RAY DIFFRACTIONr_scbond_it2.8943452
X-RAY DIFFRACTIONr_scangle_it4.4144.5694
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 9
Rwork0.339 263

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