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- PDB-3r86: Crystal structure of d(CCGGTACCGG)2 as B-DNA duplex grown with 5 ... -

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Basic information

Entry
Database: PDB / ID: 3r86
TitleCrystal structure of d(CCGGTACCGG)2 as B-DNA duplex grown with 5 mM CoCl2
ComponentsDNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
KeywordsDNA / Duplex
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Gautham, N.
CitationJournal: To be Published
Title: Crystal structure of d(CCGGTACCGG)2 as B-DNA duplex
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionMar 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_atom_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.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
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: DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2695
Polymers6,0922
Non-polymers1773
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-3 kcal/mol
Surface area3810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.756, 32.756, 93.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: DNA chain DNA (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: Chemically synthesized
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM DNA, 50mM Sodium Cacodylate buffer, 5mM CoCl2,1mM Spermine, 50% 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: BM14 / Wavelength: 1.604 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2010
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.604 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.485
11h+k,-k,-l20.515
ReflectionResolution: 2.8→28.4 Å / Num. all: 1410 / Num. obs: 1382 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 67.3 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.047 / Net I/σ(I): 3.7
Reflection shellResolution: 2.803→2.873 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.4 / Num. unique all: 77 / Rsym value: 0.402 / % possible all: 99

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
REFMAC5.5.0109refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B-DNA fiber model

Resolution: 2.8→28.37 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 21.376 / SU ML: 0.384 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27001 72 5.2 %RANDOM
Rwork0.26004 ---
all0.27561 1410 --
obs0.27561 1310 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.978 Å2
Baniso -1Baniso -2Baniso -3
1--7.96 Å20 Å20 Å2
2---7.96 Å20 Å2
3---15.92 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 3 11 418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.021452
X-RAY DIFFRACTIONr_angle_refined_deg3.93694
X-RAY DIFFRACTIONr_chiral_restr0.1830.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02210
LS refinement shellResolution: 2.803→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.892 7 -
Rwork0.655 77 -
obs-77 84.85 %

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