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- PDB-2avh: G4T3G4 dimeric quadruplex structure -

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Basic information

Entry
Database: PDB / ID: 2avh
TitleG4T3G4 dimeric quadruplex structure
Components5'-D(*GP*GP*GP*GP*TP*TP*TP*GP*GP*GP*G)-3'
KeywordsDNA / quadruplex / loop
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHazel, P. / Parkinson, G.N. / Neidle, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex.
Authors: Hazel, P. / Parkinson, G.N. / Neidle, S.
History
DepositionAug 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,6585
Polymers3,5011
Non-polymers1564
Water97354
1
A: 5'-D(*GP*GP*GP*GP*TP*TP*TP*GP*GP*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,31510
Polymers7,0032
Non-polymers3138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x+1/2,-y+3/2,z1
Unit cell
Length a, b, c (Å)29.932, 37.112, 43.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-13-

K

21A-20-

HOH

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Components

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


Mass: 3501.267 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.83 Å3/Da / Density % sol: 32.14 %
Crystal growTemperature: 284.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium iodide, sodium cacodylate, PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 284.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium iodide11
2sodium cacodylate11
3PEG 40011
4H2O11
5sodium iodide12
6sodium cacodylate12
7PEG 40012
8H2O12

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 4066 / Num. obs: 4066 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.054 / Χ2: 1.121
Reflection shellResolution: 1.5→1.54 Å / % possible obs: 98.7 % / Num. measured obs: 390 / Χ2: 0.365 / % possible all: 96.127

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Phasing

Phasing MRRfactor: 0.645 / Cor.coef. Fo:Fc: 0.232
Highest resolutionLowest resolution
Translation3.5 Å25 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GGGG(+U)TTGGGG chain A (P21)

Resolution: 1.5→23.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.752 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.208 184 4.5 %RANDOM
Rwork0.198 ---
all0.199 4065 --
obs0.199 4065 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--0.49 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 233 4 54 291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.021262
X-RAY DIFFRACTIONr_angle_refined_deg1.153406
X-RAY DIFFRACTIONr_chiral_restr0.0490.243
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02126
X-RAY DIFFRACTIONr_nbd_refined0.310.290
X-RAY DIFFRACTIONr_nbtor_refined0.2720.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.238
X-RAY DIFFRACTIONr_metal_ion_refined0.060.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3750.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.222
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0960.24
X-RAY DIFFRACTIONr_scbond_it1.033282
X-RAY DIFFRACTIONr_scangle_it1.5174.5406
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 11 -
Rwork0.299 262 -
obs--96.127 %

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