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- PDB-4r49: Racemic crystal structure of a calcium-bound B-DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4r49
TitleRacemic crystal structure of a calcium-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: 1.28 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_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.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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,41911
Polymers6,0922
Non-polymers3279
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.263, 33.604, 36.820
Angle α, β, γ (deg.)103.32, 101.02, 109.78
Int Tables number2
Space group name H-MP-1
Components on special symmetry positions
IDModelComponents
11B-105-

NA

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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.: 2 / Source method: obtained synthetically / Details: B-DNA Duplex / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 mM DNA, 50 mM sodium cacodylate, 2 M calcium chloride, 1 mM spermine, 40% 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: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.28→34.25 Å / Num. all: 25176 / Num. obs: 23975 / % possible obs: 95.23 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 47.43 Å2 / Rmerge(I) obs: 0.0372 / Net I/σ(I): 9.69
Reflection shellResolution: 1.28→1.32 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.2656 / Mean I/σ(I) obs: 2.39 / % possible all: 91.68

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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: 1.28→34.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.437 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25957 1230 5.1 %RANDOM
Rwork0.21655 ---
obs0.21889 22744 95.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.318 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0.61 Å20.54 Å2
2---0.47 Å2-0.33 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.28→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 9 167 580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.011452
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.157694
X-RAY DIFFRACTIONr_chiral_restr0.110.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0310.02210
X-RAY DIFFRACTIONr_rigid_bond_restr7.1523452
X-RAY DIFFRACTIONr_sphericity_free25.39856
X-RAY DIFFRACTIONr_sphericity_bonded12.8445574
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 79 -
Rwork0.325 1638 -
obs--91.14 %

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