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- PDB-2o4f: Structure of a parallel-stranded guanine tetraplex crystallised w... -

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Basic information

Entry
Database: PDB / ID: 2o4f
TitleStructure of a parallel-stranded guanine tetraplex crystallised with monovalent ions
Components5'-D(*TP*GP*GP*GP*GP*T)-3'
KeywordsDNA / QUADRUPLE HELIX / PARALLEL-STRANDED
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCreze, C. / Rinaldi, B. / Haser, R. / Bouvet, P. / Gouet, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ions.
Authors: Creze, C. / Rinaldi, B. / Haser, R. / Bouvet, P. / Gouet, P.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*GP*GP*GP*GP*T)-3'
B: 5'-D(*TP*GP*GP*GP*GP*T)-3'
C: 5'-D(*TP*GP*GP*GP*GP*T)-3'
D: 5'-D(*TP*GP*GP*GP*GP*T)-3'
E: 5'-D(*TP*GP*GP*GP*GP*T)-3'
F: 5'-D(*TP*GP*GP*GP*GP*T)-3'
G: 5'-D(*TP*GP*GP*GP*GP*T)-3'
H: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,21016
Polymers15,0428
Non-polymers1688
Water4,107228
1
A: 5'-D(*TP*GP*GP*GP*GP*T)-3'
B: 5'-D(*TP*GP*GP*GP*GP*T)-3'
C: 5'-D(*TP*GP*GP*GP*GP*T)-3'
D: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6209
Polymers7,5214
Non-polymers995
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*TP*GP*GP*GP*GP*T)-3'
F: 5'-D(*TP*GP*GP*GP*GP*T)-3'
G: 5'-D(*TP*GP*GP*GP*GP*T)-3'
H: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5907
Polymers7,5214
Non-polymers693
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.920, 57.370, 35.920
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 1880.251 Da / Num. of mol.: 8 / Source method: obtained synthetically
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1.82 Å3/Da / Density % sol: 32.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8 M lithium sulphate, 0.01 M magnesium sulphate, 0.05 M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1lithium sulphate11
2magnesium sulphate11
3sodium cacodylate11
4H2O11
5lithium sulphate12
6magnesium sulphate12
7sodium cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 16, 2006 / Details: mirrors
RadiationMonochromator: horizontally diffracting Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. all: 18195 / Num. obs: 17547 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.142 / Net I/σ(I): 7.05
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.71 / Num. unique all: 2977 / Rsym value: 0.227 / % possible all: 93.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 352D

352d


Resolution: 1.5→14.68 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 690707.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 851 4.9 %RANDOM
Rwork0.204 ---
all0.206 17910 --
obs0.206 17319 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.627 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 13 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-1.23 Å2
2--4.52 Å20 Å2
3----4.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.5→14.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1000 8 228 1236
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d0
X-RAY DIFFRACTIONc_improper_angle_d1.53
X-RAY DIFFRACTIONc_mcbond_it8.21.5
X-RAY DIFFRACTIONc_mcangle_it3.422
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 162 5.8 %
Rwork0.33 2621 -
obs-2783 93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2dna-rna-allatom.paramdna-rna-allatom.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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