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- PDB-4r44: Racemic crystal structure of a tetramolecular DNA G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 4r44
TitleRacemic crystal structure of a tetramolecular DNA G-quadruplex
Components5'-D(*TP*GP*GP*GP*GP*T)-3'
KeywordsDNA / racemic DNA / racemates
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.695 Å
AuthorsMandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Racemic DNA crystallography.
Authors: Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Sep 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_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

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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'
I: 5'-D(*TP*GP*GP*GP*GP*T)-3'
J: 5'-D(*TP*GP*GP*GP*GP*T)-3'
K: 5'-D(*TP*GP*GP*GP*GP*T)-3'
L: 5'-D(*TP*GP*GP*GP*GP*T)-3'
M: 5'-D(*TP*GP*GP*GP*GP*T)-3'
N: 5'-D(*TP*GP*GP*GP*GP*T)-3'
O: 5'-D(*TP*GP*GP*GP*GP*T)-3'
P: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,72334
Polymers30,08416
Non-polymers63918
Water181
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'
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)15,31615
Polymers15,0428
Non-polymers2747
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: 5'-D(*TP*GP*GP*GP*GP*T)-3'
J: 5'-D(*TP*GP*GP*GP*GP*T)-3'
K: 5'-D(*TP*GP*GP*GP*GP*T)-3'
L: 5'-D(*TP*GP*GP*GP*GP*T)-3'
M: 5'-D(*TP*GP*GP*GP*GP*T)-3'
N: 5'-D(*TP*GP*GP*GP*GP*T)-3'
O: 5'-D(*TP*GP*GP*GP*GP*T)-3'
P: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,40819
Polymers15,0428
Non-polymers36611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.940, 39.000, 84.080
Angle α, β, γ (deg.)103.34, 103.37, 90.04
Int Tables number2
Space group name H-MP-1

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Components

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


Mass: 1880.251 Da / Num. of mol.: 16 / Source method: obtained synthetically / Details: Tetramolecular G-Quadruplex / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: 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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 1 mM DNA, 50 mM potassium cacodylate, 40 mM potassium chloride, 100 mM magnesium chloride hexahydrate, 1.7 M 1,6-hexanediol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 26, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.695→37.886 Å / Num. all: 12894 / Num. obs: 12597 / % possible obs: 97.69 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 49.77 Å2 / Rmerge(I) obs: 0.1643 / Net I/σ(I): 1.7
Reflection shellResolution: 2.695→2.79 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.4338 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1292 / % possible all: 97.34

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.8.0049refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 352D

352d


Resolution: 2.695→37.886 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.879 / SU B: 7.219 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.32532 680 5.4 %RANDOM
Rwork0.29388 ---
obs0.29544 11917 97.39 %-
all-11237 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.827 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20.01 Å20.03 Å2
2---0.02 Å2-0.01 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.695→37.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1706 18 1 1725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0111914
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.1152936
X-RAY DIFFRACTIONr_chiral_restr0.0970.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02912
LS refinement shellResolution: 2.695→2.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 48 -
Rwork0.328 910 -
obs--96.38 %

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