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- PDB-2gwq: Crystal structure of D(G4T4G4) with four quadruplexes in the asym... -

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Basic information

Entry
Database: PDB / ID: 2gwq
TitleCrystal structure of D(G4T4G4) with four quadruplexes in the asymmetric unit.
Components5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
KeywordsDNA / OXYTRICHA / G-QUARTET / G-QUADRUPLEX / G-TETRAD / G-TETRAPLEX / FOUR QUADRUPLEXES / ASYMMETRIC UNIT.
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, M.P.H. / Parkinson, G.N. / Neidle, S.
CitationJournal: To be Published
Title: Crystal structure of D(G4T4G4) with four and six quadruplexes in the asymmetric unit.
Authors: Lee, M.P.H. / Haider, S. / Parkinson, G.N. / Neidle, S.
History
DepositionMay 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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.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_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*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
B: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
C: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
D: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
E: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
F: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
G: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
H: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,22628
Polymers30,4448
Non-polymers78220
Water3,045169
1
A: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
B: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8067
Polymers7,6112
Non-polymers1955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
D: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8067
Polymers7,6112
Non-polymers1955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
F: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8067
Polymers7,6112
Non-polymers1955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
H: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8067
Polymers7,6112
Non-polymers1955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.332, 53.470, 97.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3805.460 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: OXYTRICHA NOVA TELOMERIC SEQUENCE
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 285 K / pH: 6.5
Details: MAGNESIUM CHLORIDE, DNA, POTASSIUM CHLORIDE, MPD, PEPTIDE CONJUGATE BIS RKKV ACRIDONE, SPERMINE TETRAHYDROCHLORIDE, POTASSIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING DROP, temperature 285K, pH 6.50
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM CHLORIDE11
2POTASSIUM CHLORIDE11
3MPD11
4SPERMINE TETRAHYDROCHLORIDE11
5POTASSIUM CACODYLATE11
6H2O11
7MAGNESIUM CHLORIDE12
8POTASSIUM CHLORIDE12
9MPD12
10POTASSIUM CACODYLATE12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.862451
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2003 / Details: A CYLINDRICAL GRAZING INCIDENCE MIRROR
RadiationMonochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.862451 Å / Relative weight: 1
ReflectionResolution: 2→17 Å / Num. obs: 18992 / % possible obs: 96.6 % / Observed criterion σ(I): -2 / Redundancy: 3.35 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 26.27
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 8.74 / % possible all: 96.8

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Processing

Software
NameClassification
ADSCdata collection
DENZOdata reduction
EPMRphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DNA PART OF NDB ENTRY CODE UD0014 OR PDB ENTRY CODE 1JRN.

1jrn


Resolution: 2→8 Å / Num. parameters: 8867 / Num. restraintsaints: 10018 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1850 9.989 %RANDOM
all0.233 18520 --
obs0.231 -91.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 17.84 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2213
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2024 20 169 2213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.003
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.005
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.07
X-RAY DIFFRACTIONs_approx_iso_adps0

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