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- PDB-1qyl: GCATGCT + Vanadium -

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Basic information

Entry
Database: PDB / ID: 1qyl
TitleGCATGCT + Vanadium
Components5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
KeywordsDNA / Quadruplex DNA
Function / homologyVANADIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1 Å
AuthorsCardin, C.J. / Gan, Y. / Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Moraes, M.I.A.
CitationJournal: To be Published
Title: Metal Ion Distribution and Stabilisation of the DNA Quadruplex Structure Formed by d(GCATGCT)
Authors: Cardin, C.J. / GAN, Y. / Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Moraes, M.I.A.
History
DepositionSep 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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 1.4Apr 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*CP*AP*TP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1642
Polymers2,1131
Non-polymers511
Water81145
1
A: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
hetero molecules

A: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
hetero molecules

A: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
hetero molecules

A: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6578
Polymers8,4544
Non-polymers2044
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)22.532, 58.469, 24.148
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-8-

V

21A-100-

HOH

31A-103-

HOH

41A-119-

HOH

51A-124-

HOH

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Components

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


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-V / VANADIUM ION / Vanadium


Mass: 50.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: V
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.81 Å3/Da / Density % sol: 32.16 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: NaCacodylate, Vanadium Chloride, Sodium Chloride, MPD, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaCacodylate11
2Vanadium Chloride11
3Sodium Chloride11
4MPD11
5H2O11
6NaCacodylate12
7Vanadium Chloride12
8MPD12
9H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8416 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8416 Å / Relative weight: 1
ReflectionResolution: 1→5.8 Å / Num. obs: 8848 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.095 / Net I/σ(I): 20.1
Reflection shellResolution: 1→1.2 Å / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 12.63 / Num. unique all: 3718 / % possible all: 100

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
XTALVIEWrefinement
RefinementMethod to determine structure: AB INITIO
Starting model: NDB entry udg028

Resolution: 1→5.8 Å / Num. parameters: 1655 / Num. restraintsaints: 1425 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 311 3.7 %RANDOM
Rwork0.1493 ---
obs0.1493 8406 98.4 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 180.5
Refinement stepCycle: LAST / Resolution: 1→5.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 140 1 45 186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.023
X-RAY DIFFRACTIONs_angle_d0.042
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0036
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0

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