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- PDB-2hri: A parallel stranded human telomeric quadruplex in complex with th... -

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Basic information

Entry
Database: PDB / ID: 2hri
TitleA parallel stranded human telomeric quadruplex in complex with the porphyrin TMPyP4
Components5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3'
KeywordsDNA / QUADRUPLEX / PROPELLER / DIMERIC / HUMAN TELOMERE PARALLEL STRANDED / LIGAND / COMPLEX
Function / homology: / Chem-POH / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsParkinson, G.N. / Ghosh, R. / Neidle, S.
CitationJournal: Biochemistry / Year: 2007
Title: Structural basis for binding of porphyrin to human telomeres.
Authors: Parkinson, G.N. / Ghosh, R. / Neidle, S.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 / pdbx_struct_special_symmetry / 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.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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,4137
Polymers6,9392
Non-polymers1,4755
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.290, 61.990, 61.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-24-

K

21A-26-

POH

31A-26-

POH

41A-69-

HOH

51B-63-

HOH

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Components

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


Mass: 3469.269 Da / Num. of mol.: 2 / Fragment: Telomere / 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: Chemical ChemComp-POH / (1Z,4Z,9Z,15Z)-5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)-21,23-dihydroporphyrin / TMPyP4


Mass: 678.826 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H38N8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 6.5
Details: 500 mM ammonium sulphate, 80 mM lithium sulphate, 80 mM sodium chloride, 80 mM potassium chloride, 20mM potassium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 285K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulphate11
2lithium sulphate11
3sodium chloride11
4potassium chloride11
5potassium cacodylate11
6H2O11
7ammonium sulphate12
8lithium sulphate12
9sodium chloride12
10potassium chloride12
11potassium cacodylate12
12H2O12

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 7, 2006 / Details: osmic mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→28.35 Å / Num. all: 4443 / Num. obs: 4443 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.07 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.2
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 6.5 / Num. unique all: 433 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A5R

2a5r


Resolution: 2.09→28.35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.389 / SU ML: 0.122 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24833 204 4.6 %RANDOM
Rwork0.19829 ---
all0.20062 4239 --
obs0.20062 4239 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.671 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å20 Å2
2--2.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.09→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 462 107 46 615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.163980
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02364
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3220.2181
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2343
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it1.8743724
X-RAY DIFFRACTIONr_scangle_it2.5774.5980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.611 13 -
Rwork0.364 309 -
obs--99.38 %

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