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- PDB-1s9b: Crystal Structure Analysis of the B-DNA GAATTCG -

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Basic information

Entry
Database: PDB / ID: 1s9b
TitleCrystal Structure Analysis of the B-DNA GAATTCG
Components5'-D(*GP*AP*AP*TP*TP*CP*G)-3'
KeywordsDNA / DOUBLE HELIX / CUBIC DNA / NICKEL
Function / homologyNICKEL (II) ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.81 Å
AuthorsValls, N. / Uson, I. / Gouyette, C. / Subirana, J.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: A cubic arrangement of DNA double helices based on nickel-guanine interactions
Authors: Valls, N. / Uson, I. / Gouyette, C. / Subirana, J.A.
History
DepositionFeb 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,5106
Polymers4,2752
Non-polymers2354
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.867, 70.867, 70.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DG / End label comp-ID: DG / Refine code: _ / Auth seq-ID: 1 - 7 / Label seq-ID: 1 - 7

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 2137.435 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, Nickel Chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Nickel Chloride11
3cacodylate11
4H2O11
5MPD12
6Nickel Chloride12
7H2O12

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1411
SYNCHROTRONESRF BM1421.48475, 1.48563, 1.31155
Detector
TypeIDDetectorDate
MARRESEARCH1CCDSep 10, 2002
MARRESEARCH2CCDSep 10, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.484751
31.485631
41.311551
ReflectionResolution: 2.81→22.4 Å / Num. obs: 1491 / % possible obs: 97.4 % / Rsym value: 0.095

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD
Starting model: ideal B-DNA

Resolution: 2.81→22.4 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.09 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 1.15 / ESU R Free: 0.361
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.26428 69 4.7 %RANDOM
Rwork0.281 ---
all0.281 ---
obs0.281 1388 95.73 %-
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: 36.94 Å2
Refinement stepCycle: LAST / Resolution: 2.81→22.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 284 4 20 308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023396
X-RAY DIFFRACTIONr_angle_refined_deg3.1243488
X-RAY DIFFRACTIONr_chiral_restr0.10.242
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02150
X-RAY DIFFRACTIONr_nbd_refined0.2310.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.28
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.22
X-RAY DIFFRACTIONr_mcbond_it0.5681.535
X-RAY DIFFRACTIONr_scbond_it2.893325
X-RAY DIFFRACTIONr_scangle_it4.734.5488
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 142 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.070.05
tight thermal0.210.5
LS refinement shellResolution: 2.815→2.887 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.899 3
Rwork0.425 54

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