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- PDB-4r4d: Racemic crystal structure of a magnesium-bound B-DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4r4d
TitleRacemic crystal structure of a magnesium-bound B-DNA duplex
Components5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
KeywordsDNA / racemic DNA / racemates
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_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(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
C: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
D: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,40113
Polymers12,1844
Non-polymers2179
Water2,414134
1
A: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2388
Polymers6,0922
Non-polymers1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
D: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1645
Polymers6,0922
Non-polymers723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.610, 32.951, 46.250
Angle α, β, γ (deg.)70.76, 80.77, 73.77
Int Tables number2
Space group name H-MP-1

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Components

#1: DNA chain
5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'


Mass: 3045.992 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: B-DNA duplex / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.79 Å3/Da / Density % sol: 31.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 mM DNA, 50 mM sodium cacodylate, 200 mM magnesium chloride, 2.5 mM spermine, 30% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.29→43.54 Å / Num. all: 42395 / Num. obs: 38749 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 47.68 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 14.11
Reflection shellResolution: 1.29→1.37 Å / % possible all: 86.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R86

3r86


Resolution: 1.29→43.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.747 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3113 1979 5 %RANDOM
Rwork0.2689 ---
obs0.2709 37851 94.19 %-
all-40186 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.2 Å2-0.03 Å2
2---0.54 Å20.16 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.29→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 9 134 951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0111087
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2981.161678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0280.02503
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr9.98931087
X-RAY DIFFRACTIONr_sphericity_free14.304515
X-RAY DIFFRACTIONr_sphericity_bonded10.35651096
LS refinement shellResolution: 1.29→1.326 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 137 -
Rwork0.329 2522 -
obs--85.06 %

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