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- PDB-1v3p: Crystal structure of d(GCGAGAGC): the DNA octaplex structure with... -

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Basic information

Entry
Database: PDB / ID: 1v3p
TitleCrystal structure of d(GCGAGAGC): the DNA octaplex structure with I-motif of G-quartet
Components5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
KeywordsDNA / octaplex / quadruplex / G-quartet / I-motif / I-motif of G-quartet / base-intercalated duplex / base-intercalated motif / sheared G:A pair / deoxyribonucleic acid / X-ray analysis
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKondo, J. / Umeda, S. / Sunami, T. / Takenaka, A.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats
Authors: Kondo, J. / Adachi, W. / Umeda, S. / Sunami, T. / Takenaka, A.
History
DepositionNov 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
B: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2834
Polymers5,2052
Non-polymers782
Water1,74797
1
A: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
B: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
hetero molecules

A: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
B: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
hetero molecules

A: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
B: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
hetero molecules

A: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
B: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,13316
Polymers20,8208
Non-polymers3138
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)36.180, 36.380, 63.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-114-

K

21B-115-

K

31A-17-

HOH

41A-64-

HOH

51B-75-

HOH

DetailsThe biological assembly is an octaplex generated from the duplex in the asymmetric unit by the operations: (x, y, z), (1-x, 1-y, z), (x,1-y,2-z) and (1-x, y, 2-z).

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Components

#1: DNA chain 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'


Mass: 2602.540 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.91 Å3/Da / Density % sol: 35.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2-methyl-2,4-pentanediol, spermine tetrahydrochloride, sodium chloride, potassium chloride, sodium cacodylate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
12-methyl-2,4-pentanediol11
2spermine tetrahydrochloride11
3sodium chloride11
4potassium chloride11
5sodium cacodylate11
6sodium chloride12
7potassium chloride12
8sodium cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 2014 / Num. obs: 1980 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.4 / Num. unique all: 199 / % possible all: 99

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALAdata scaling
AMoREphasing
CNS1refinement
CrystalClear(MSC/RIGAKU)data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V3N

1v3n


Resolution: 2.3→9 Å / σ(F): 3
Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
RfactorNum. reflectionSelection details
Rfree0.265 174 RANDOM
Rwork0.234 --
all-1972 -
obs-1903 -
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 332 2 97 431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.368 14 -
Rwork0.37 --
obs--87.1 %

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