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- PDB-3ggk: Locating monovalent cations in one turn of G/C rich B-DNA -

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Basic information

Entry
Database: PDB / ID: 3ggk
TitleLocating monovalent cations in one turn of G/C rich B-DNA
Components5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G) -3'
KeywordsDNA / CATIONS / DIVALENT CATIONS / MONOVALENT CATIONS / RUBIDIUM ION
Function / homologyRUBIDIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.87 Å
AuthorsMaehigashi, T. / Moulaei, T. / Watkins, D. / Komeda, S. / Williams, L.D.
CitationJournal: To be Published
Title: Locating monovalent cations in one turn of G/C rich B-DNA
Authors: Maehigashi, T. / Moulaei, T. / Watkins, D. / Komeda, S. / Williams, L.D.
History
DepositionFeb 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G) -3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3388
Polymers3,0461
Non-polymers2927
Water2,180121
1
A: 5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G) -3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,67716
Polymers6,0922
Non-polymers58514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1340 Å2
ΔGint-34 kcal/mol
Surface area3980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.135, 25.156, 34.113
Angle α, β, γ (deg.)90.00, 116.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-25-

MG

21A-101-

RB

31A-220-

HOH

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Components

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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, Magnesium acetate, Rubidium acetate, Rubidium hydroxide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Magnesium acetate11
3Rubidium acetate11
4Rubidium hydroxide11
5MPD12
6Magnesium acetate12
7Rubidium acetate12
8Rubidium hydroxide12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.81528 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2004
RadiationMonochromator: Cryogenically cooled Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81528 Å / Relative weight: 1
ReflectionResolution: 0.784→30.6 Å / Num. obs: 19281 / % possible obs: 63.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 23

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DNA coordinates from PDB Entry 1bd1 (Heinemann and Alings)

1bd1


Resolution: 0.87→30.6 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.377 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1343 1047 5.6 %RANDOM
Rwork0.1188 ---
obs0.11971 17543 90.55 %-
all-17543 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.764 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.14 Å2
2---0.14 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 0.87→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 287 10 156 453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021376
X-RAY DIFFRACTIONr_angle_refined_deg1.8333640
X-RAY DIFFRACTIONr_chiral_restr0.1040.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.02126
X-RAY DIFFRACTIONr_nbd_refined0.220.283
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.244
X-RAY DIFFRACTIONr_scbond_it1.3393523
X-RAY DIFFRACTIONr_scangle_it1.6334.5614
X-RAY DIFFRACTIONr_rigid_bond_restr0.8393523
X-RAY DIFFRACTIONr_sphericity_free3.4013110
X-RAY DIFFRACTIONr_sphericity_bonded3.6473343
LS refinement shellResolution: 0.865→0.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 46 -
Rwork0.199 714 -
obs-760 50.26 %

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