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- PDB-1k8p: Structure of the Human G-quadruplex reveals a novel topology -

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Basic information

Entry
Database: PDB / ID: 1k8p
TitleStructure of the Human G-quadruplex reveals a novel topology
Components5'-D(*(BRU)P*AP*GP*GP*GP*(BRU)P*TP*AP*GP*GP*GP*T)-3'
KeywordsDNA / quadruplex DNA / double chain reversal loop / dimeric quadruplex / Human telomere sequence / G(anti).G(anti).G(anti).G(anti) / parallel stranded
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.4 Å
AuthorsParkinson, G.N. / Lee, M.P.H. / Neidle, S.
Citation
Journal: Nature / Year: 2002
Title: Crystal structure of parallel quadruplexes from human telomeric DNA.
Authors: Parkinson, G.N. / Lee, M.P. / Neidle, S.
#1: Journal: PATENT / Year: 2002
Title: Crystal Structure of G-quadruplex
Authors: Parkinson, G.N. / Lee, M.P.H. / Neidle, S.
History
DepositionOct 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues ...pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _citation.country / _citation.pdbx_database_id_patent ..._citation.country / _citation.pdbx_database_id_patent / _citation.title / _citation.year / _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.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.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.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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*(BRU)P*AP*GP*GP*GP*(BRU)P*TP*AP*GP*GP*GP*T)-3'
B: 5'-D(*(BRU)P*AP*GP*GP*GP*(BRU)P*TP*AP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9085
Polymers7,8062
Non-polymers1013
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.607, 56.607, 40.546
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: DNA chain 5'-D(*(BRU)P*AP*GP*GP*GP*(BRU)P*TP*AP*GP*GP*GP*T)-3'


Mass: 3903.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#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 / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, KCl, LiCl, MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3LiCl11
4MgCl211
5MPD12
Crystal grow
*PLUS
Temperature: 285 K / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 %ammonium sulfate gradient1reservoir
2500 mMammonium sulfate1drop
350 mM1dropNaCl
450 mM1dropKCl
550 mM1dropLi2SO4
60.5 mMDNA1drop
750 mMpotassium cacodylate1droppH6.5

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2001 / Details: Osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→26 Å / Num. all: 3130 / Num. obs: 2870 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 9.6 / Num. unique all: 294 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 3130 / % possible obs: 99.2 % / Num. measured all: 64877

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→10 Å / σ(F): 0 / Stereochemistry target values: Parkinson et al.
RfactorNum. reflectionSelection details
Rfree0.28 286 Random
Rwork0.189 --
all0.197 3029 -
obs0.193 2572 -
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 498 7 50 555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.016
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_from_restr_planes0.012
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor obs: 0.186 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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