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- PDB-1qzl: GCATGCT + Cobalt -

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Basic information

Entry
Database: PDB / ID: 1qzl
TitleGCATGCT + Cobalt
Components5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
KeywordsDNA / DNA quadruplex
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 17, 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 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,1722
Polymers2,1131
Non-polymers591
Water181
1
X: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)8,6898
Polymers8,4544
Non-polymers2364
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_555x,x-y,-z+1/31
Unit cell
Length a, b, c (Å)24.789, 24.789, 91.818
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
11X-102-

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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.86 Å3/Da / Density % sol: 33.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium cacodylate, Cobalt dichloride, potassium chloride, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2Cobalt dichloride11
3potassium chloride11
4MPD11
5H2O11
6sodium cacodylate12
7Cobalt dichloride12
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: 2.85→30.606 Å / Num. obs: 522 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 41.857 Å2 / Rmerge(I) obs: 0.1573 / Rsym value: 0.1507 / Net I/σ(I): 4.1
Reflection shellResolution: 2.85→3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 2.1 / Num. unique all: 69 / Rsym value: 0.288 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→30.57 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.819 / SU B: 7.852 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.047 / ESU R Free: 0.525 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33473 23 4.5 %RANDOM
Rwork0.23978 ---
all0.24375 522 --
obs0.24375 489 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.898 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.85→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 140 1 1 142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021156
X-RAY DIFFRACTIONr_bond_other_d0.0020.0269
X-RAY DIFFRACTIONr_angle_refined_deg2.9093239
X-RAY DIFFRACTIONr_angle_other_deg1.4213173
X-RAY DIFFRACTIONr_chiral_restr0.1410.221
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022
X-RAY DIFFRACTIONr_nbd_refined0.1240.211
X-RAY DIFFRACTIONr_nbd_other0.2270.259
X-RAY DIFFRACTIONr_nbtor_other0.1150.233
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.27
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.239 2
Rwork0.202 27

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