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- PDB-3pbx: Strontium bound to the sequence d(CCGGCGCCGG) -

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Basic information

Entry
Database: PDB / ID: 3pbx
TitleStrontium bound to the sequence d(CCGGCGCCGG)
ComponentsDNA
KeywordsDNA / Holliday junction (higher order DNA structure) / Intermediate formed in Homologous recombination
Function / homologySTRONTIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.879 Å
AuthorsNaseer, A. / Cardin, C.J.
CitationJournal: To be Published
Title: Strontium bound to the sequence d(CCGGCGCCGG)
Authors: Naseer, A. / Cardin, C.J.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Database references / Refinement description / Structure summary
Category: audit_author / citation_author / software
Item: _audit_author.name / _citation_author.name / _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: DNA
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2054
Polymers6,0942
Non-polymers1112
Water1,02757
1
A: DNA
B: DNA
hetero molecules

A: DNA
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4098
Polymers12,1884
Non-polymers2214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3610 Å2
ΔGint-79 kcal/mol
Surface area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.890, 25.001, 37.044
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-36-

HOH

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Components

#1: DNA chain DNA


Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
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: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Feb 10, 2007 / Details: multi-graded optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.879→14.866 Å / Num. all: 4705 / Num. obs: 3706 / % possible obs: 78.55 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Biso Wilson estimate: 27.446 Å2 / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.879→1.927 Å

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Processing

Software
NameVersionClassification
CrysalisProReddata collection
MOLREPphasing
REFMAC5.2.0005refinement
CrysalisProReddata reduction
CrysalisProReddata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GOJ

3goj


Resolution: 1.879→14.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.872 / SU B: 5.747 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32701 175 4.7 %RANDOM
Rwork0.2508 ---
obs0.2544 3531 78.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.446 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å20 Å20.31 Å2
2--3.36 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.879→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 2 57 463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021452
X-RAY DIFFRACTIONr_angle_refined_deg3.6663694
X-RAY DIFFRACTIONr_chiral_restr0.150.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02210
X-RAY DIFFRACTIONr_nbd_refined0.2590.2130
X-RAY DIFFRACTIONr_nbtor_refined0.3440.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3890.236
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4340.225
X-RAY DIFFRACTIONr_scbond_it3.0073546
X-RAY DIFFRACTIONr_scangle_it4.0164.5694
LS refinement shellResolution: 1.879→1.927 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 2 -
Rwork0.477 25 -
obs--7.69 %

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