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- PDB-5dnb: STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-G-T-T-G-G AND COMPARISON... -

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Basic information

Entry
Database: PDB / ID: 5dnb
TitleSTRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-G-T-T-G-G AND COMPARISON WITH ISOMORPHOUS DECAMERS C-C-A-A-G-A-T-T-G-G AND C-C-A-G-G-C-C-T-G-G
ComponentsDNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsPrive, G.G. / Yanagi, K. / Dickerson, R.E.
CitationJournal: J.Mol.Biol. / Year: 1991
Title: Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G.
Authors: Prive, G.G. / Yanagi, K. / Dickerson, R.E.
History
DepositionMar 22, 1990Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1425
Polymers3,0451
Non-polymers974
Water1,38777
1
A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,28410
Polymers6,0902
Non-polymers1948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)32.250, 25.530, 34.380
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: THESE WATER MOLECULES MAKE A SPLINE OF HYDRATION. / 2: THESE WATER MOLECULES MAKE A SPLINE OF HYDRATION. / 3: THESE WATER MOLECULES MAKE A SPLINE OF HYDRATION. / 4: HOH 63 IS ONLY 1.57 ANGSTROMS FROM THE O4* OF A 8.
Components on special symmetry positions
IDModelComponents
11A-12-

MG

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Components

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


Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4WATER12
5MPD12
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlDNA1drop
20.76 M1dropMgCl2
360 %MPD1reservoir
41
51

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→8 Å / Num. obs: 4402 / Observed criterion σ(I): 1

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.4→8 Å / σ(F): 1 /
RfactorNum. reflection
obs0.16 4402
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 4 77 283
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it2.14
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it48
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0210.03
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0290.03
X-RAY DIFFRACTIONn_phos_bond_d0.0250.025
X-RAY DIFFRACTIONn_phos_bond_angle_d0.050.06
X-RAY DIFFRACTIONn_plane_restr0.020.02
X-RAY DIFFRACTIONn_chiral_restr0.0980.1
X-RAY DIFFRACTIONn_singtor_nbd0.0740.2
X-RAY DIFFRACTIONn_multtor_nbd0.1210.2
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.4 Å / Num. reflection all: 4402 / σ(F): 1 / Rfactor all: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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