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- PDB-1kf1: Structure and Packing of Human Telomeric DNA -

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Basic information

Entry
Database: PDB / ID: 1kf1
TitleStructure and Packing of Human Telomeric DNA
Components5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3
KeywordsDNA / QUADRUPLEX DNA / DOUBLE CHAIN REVERSAL LOOP / HUMAN TELOMERE SEQUENCE / G(ANTI).G(ANTI).G(ANTI) / PARALLEL STRANDED
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionNov 19, 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: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_dist_value / _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_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
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,1014
Polymers6,9831
Non-polymers1173
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.682, 56.682, 42.106
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-26-

K

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Components

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


Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 400, potassium iodide, potassium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2KI11
3KCl11

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.901 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 4495 / Num. obs: 4304 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 50
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 15 / Num. unique all: 440 / % possible all: 97.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 4595 / % possible obs: 98 % / Num. measured all: 50951 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.117

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K8P

1k8p


Resolution: 2.1→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 4 / Stereochemistry target values: parkinson et al.
RfactorNum. reflectionSelection details
Rfree0.263 441 RANDOM
Rwork0.229 --
all0.235 4416 -
obs0.231 4227 -
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 465 3 68 536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.003
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_from_restr_planes0.007
LS refinement shellResolution: 2→2.09 Å / Rfactor Rwork: 0.296
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor all: 0.235 / Rfactor obs: 0.226 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rwork: 0.296

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