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- PDB-1nvy: Strontium bound to the Holliday junction sequence d(TCGGTACCGA)4 -

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Basic information

Entry
Database: PDB / ID: 1nvy
TitleStrontium bound to the Holliday junction sequence d(TCGGTACCGA)4
Componentsd(TCGGTACCGA)4
KeywordsDNA / Holliday Junction / Strontium / Sr2+
Function / homologySTRONTIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsCardin, C.J. / Thorpe, J.H. / Gale, B.C. / Teixeira, S.C.M.
CitationJournal: To be published
Title: Strontium, a MAD taerget for the DNA Holliday junction
Authors: Cardin, C.J. / Thorpe, J.H. / Gale, B.C. / Teixeira, S.C.M.
History
DepositionFeb 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 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: d(TCGGTACCGA)4
B: d(TCGGTACCGA)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5287
Polymers6,0902
Non-polymers4385
Water1,928107
1
A: d(TCGGTACCGA)4
B: d(TCGGTACCGA)4
hetero molecules

A: d(TCGGTACCGA)4
B: d(TCGGTACCGA)4
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_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)63.734, 25.320, 36.493
Angle α, β, γ (deg.)90.00, 110.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

21B-567-

HOH

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Components

#1: DNA chain d(TCGGTACCGA)4


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthezied
#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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: SrCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9470, 0.7301, 0.7667, 0.7670
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9471
20.73011
30.76671
40.7671
ReflectionResolution: 1.5→20 Å / Num. all: 16734 / Num. obs: 16734 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 20.89 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.58
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 1.88 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 4.38 / Num. unique all: 2509 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→34.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.973 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26294 433 4.9 %RANDOM
Rwork0.2069 ---
obs0.20962 8443 98.92 %-
all-8443 --
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: 17.039 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å2-0.41 Å2
2--1.15 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 5 107 516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021452
X-RAY DIFFRACTIONr_bond_other_d0.0020.02192
X-RAY DIFFRACTIONr_angle_refined_deg2.4423694
X-RAY DIFFRACTIONr_angle_other_deg1.7073484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024
X-RAY DIFFRACTIONr_nbd_refined0.130.256
X-RAY DIFFRACTIONr_nbd_other0.2280.2201
X-RAY DIFFRACTIONr_nbtor_other0.1020.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.252
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0860.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3510.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it2.8833452
X-RAY DIFFRACTIONr_scangle_it3.8074.5694
X-RAY DIFFRACTIONr_rigid_bond_restr2.0422452
X-RAY DIFFRACTIONr_sphericity_free6.9422112
X-RAY DIFFRACTIONr_sphericity_bonded5.7382404
LS refinement shellResolution: 1.5→1.581 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.31 51
Rwork0.262 1205

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