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- PDB-3qcr: Incomplete structural model of a human telomeric DNA quadruplex-a... -

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Basic information

Entry
Database: PDB / ID: 3qcr
TitleIncomplete structural model of a human telomeric DNA quadruplex-acridine complex.
ComponentsHuman telomeric repeat deoxyribonucleic acid
KeywordsDNA / quadruplex / acridine ligand-complex / telomere
Function / homology: / Chem-R14 / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCollie, G.W. / Neidle, S. / Parkinson, G.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structural basis of telomeric RNA quadruplex-acridine ligand recognition.
Authors: Collie, G.W. / Sparapani, S. / Parkinson, G.N. / Neidle, S.
History
DepositionJan 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Human telomeric repeat deoxyribonucleic acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6024
Polymers3,7731
Non-polymers8283
Water00
1
A: Human telomeric repeat deoxyribonucleic acid
hetero molecules

A: Human telomeric repeat deoxyribonucleic acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2038
Polymers7,5472
Non-polymers1,6566
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area3760 Å2
ΔGint-22 kcal/mol
Surface area3410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.674, 71.674, 29.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-14-

K

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Components

#1: DNA chain Human telomeric repeat deoxyribonucleic acid


Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Deoxyribonucleic acid synthesised by standard phosphoramidite chemistry
Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-R14 / N,N'-[acridine-3,6-diylbis(1H-1,2,3-triazole-1,4-diylbenzene-3,1-diyl)]bis[3-(diethylamino)propanamide] / triazole-acridine conjugate


Mass: 749.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H47N11O2

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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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, KCl, Na cacodylate, spermine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2010
RadiationMonochromator: double crystal (Si 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.16→29.37 Å / Num. obs: 1104 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 19.9
Reflection shellResolution: 3.16→3.26 Å / Rmerge(I) obs: 0.115 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K8P

1k8p


Resolution: 3.2→9.96 Å / Cor.coef. Fo:Fc: 0.813 / Cor.coef. Fo:Fc free: 0.686 / SU B: 52.628 / SU ML: 0.515 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R Free: 0.739 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.37837 46 5.5 %RANDOM
Rwork0.34391 ---
obs0.34595 783 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.295 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.36 Å20 Å2
2---0.73 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 3.2→9.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 222 58 0 280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021312
X-RAY DIFFRACTIONr_angle_refined_deg0.992.993472
X-RAY DIFFRACTIONr_chiral_restr0.0540.242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021170
LS refinement shellResolution: 3.2→3.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 1 -
Rwork0.265 59 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.32052.9769-2.94119.0169-4.8388.0098-0.2108-0.29880.1685-0.0650.10750.79640.83491.19370.10330.34530.01210.09410.4995-0.04990.470525.52241.9115.692
27.8701-6.591-6.6569.20744.98995.7730.24250.33540.2535-0.3736-0.01610.0457-0.2318-0.4069-0.22650.14580.0188-0.02040.217-0.02650.056514.1641.91310.684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 4
2X-RAY DIFFRACTION2A5 - 11

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