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- PDB-4r48: Racemic crystal structure of a calcium-bound DNA four-way junction -

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Basic information

Entry
Database: PDB / ID: 4r48
TitleRacemic crystal structure of a calcium-bound DNA four-way junction
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: 2.33 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 1.2Aug 28, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.3Sep 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_ncs_dom_lim
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_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_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)6,1554
Polymers6,0922
Non-polymers632
Water39622
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

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)12,3108
Polymers12,1844
Non-polymers1264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)65.950, 23.355, 72.907
Angle α, β, γ (deg.)90.00, 115.47, 90.00
Int Tables number15
Space group name H-MC12/c1
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DG / End label comp-ID: DG / Label seq-ID: 1 - 10

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1chain AAA1 - 10
2chain BBB11 - 20
DetailsOne crossing strand and one non-crossing strand form a continuous network in the crystal.

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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: DNA four-way junction / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 mM DNA, 75 mM sodium cacodylate, 30 mM calcium chloride, 1 mM spermine, 35% 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: 2.33→32.91 Å / Num. all: 4365 / Num. obs: 4156 / % possible obs: 95.23 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 49.84 Å2 / Rmerge(I) obs: 0.0442 / Net I/σ(I): 4.55
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2929 / Mean I/σ(I) obs: 1.68 / % possible all: 94.34

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Processing

Software
NameClassification
DNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DCW

1dcw


Resolution: 2.33→32.91 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3409 218 5.26 %RANDOM
Rwork0.2855 3924 --
obs0.2887 4142 99 %-
all-4184 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.77 Å2 / Biso mean: 46.5866 Å2 / Biso min: 25.23 Å2
Refinement stepCycle: LAST / Resolution: 2.33→32.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 2 22 428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01452
X-RAY DIFFRACTIONf_angle_d1.066694
X-RAY DIFFRACTIONf_chiral_restr0.0578
X-RAY DIFFRACTIONf_plane_restr0.00920
X-RAY DIFFRACTIONf_dihedral_angle_d37.048192
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A192X-RAY DIFFRACTION6.479TORSIONAL
12B192X-RAY DIFFRACTION6.479TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.33-2.93490.56941030.454319582061
2.9349-32.91360.29691150.246819662081

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