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- PDB-1mf5: GCATGCT Quadruplex -

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Basic information

Entry
Database: PDB / ID: 1mf5
TitleGCATGCT Quadruplex
Components5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
KeywordsDNA / QUADRUPLEX / ATOMIC RESOLUTION
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsThorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Cardin, C.J.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution
Authors: Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Cardin, C.J.
History
DepositionAug 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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_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_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'
B: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3883
Polymers4,2272
Non-polymers1611
Water68538
1
A: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
B: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)8,7766
Polymers8,4544
Non-polymers3222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)22.128, 59.215, 45.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-126-

HOH

21B-128-

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.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.77 Å3/Da / Density % sol: 30.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: Cobalt Hexammine, Cacodylate, MPD, NaCl, KCl, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Cobalt Hexammine11
2Cacodylate11
3MPD11
4NaCl11
5KCl11
Crystal grow
*PLUS
Temperature: 290 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mMsodium cacodylate1drop
280 mMcobalt hexammine1drop
310 %1drop
4800 mM1dropKCl
530 mM1dropNaCl
61 mMDNA1drop
730 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.1→29.62 Å / Num. obs: 12514 / % possible obs: 99.3 % / Redundancy: 7.7 % / Biso Wilson estimate: 18.213 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.96
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 6.59 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.24 / Num. unique all: 2803 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 20 Å / Num. obs: 2803 / Redundancy: 7.7 % / Num. measured all: 12514
Reflection shell
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 1.2 Å / % possible obs: 99.4 % / Redundancy: 6.64 %

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
SHELXmodel building
SHELXL-97refinement
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UDG028

Resolution: 1.1→20 Å / Num. parameters: 2924 / Num. restraintsaints: 2847 / 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
Rfree0.224 625 4.99 %RANDOM
Rwork0.2126 ---
all0.216 12514 --
obs0.216 12514 97.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 175 / Occupancy sum non hydrogen: 322
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 280 7 38 325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0018
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_cmpnt0.034
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 1.2 Å / Rfactor Rfree: 0.2173 / Rfactor Rwork: 0.208

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