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- PDB-2d25: C-C-A-G-G-C-M5C-T-G-G; HELICAL FINE STRUCTURE, HYDRATION, AND COM... -

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Basic information

Entry
Database: PDB / ID: 2d25
TitleC-C-A-G-G-C-M5C-T-G-G; HELICAL FINE STRUCTURE, HYDRATION, AND COMPARISON WITH C-C-A-G-G-C-C-T-G-G
ComponentsDNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsHeinemann, U. / Hahn, M.
Citation
Journal: J.Biol.Chem. / Year: 1992
Title: C-C-A-G-G-C-m5C-T-G-G. Helical fine structure, hydration, and comparison with C-C-A-G-G-C-C-T-G-G.
Authors: Heinemann, U. / Hahn, M.
#1: Journal: Embo J. / Year: 1991
Title: The Conformation of a B-DNA Decamer Is Mainly Determined By Its Sequence and Not By Crystal Environment
Authors: Heinemann, U. / Alings, C.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallographic Study of One Turn of G/C-Rich B-DNA
Authors: Heinemann, U. / Alings, C.
#3: Journal: Structure and Methods. DNA and RNA / Year: 1990
Title: Structural Features of G/C-Rich DNA Going a Or B
Authors: Heinemann, U. / Alings, C. / Lauble, H.
#4: Journal: Nucleosides and Nucleotides / Year: 1990
Title: X-Ray Studies of DNA Aiming at Elucidating the Sequence-Structure Code
Authors: Heinemann, U. / Alings, C. / Lauble, H.
History
DepositionApr 23, 1991Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 23, 1991Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 14, 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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: DNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1443
Polymers6,1202
Non-polymers241
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.770, 53.770, 34.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

21B-100-

HOH

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Components

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


Mass: 3060.020 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.5 / Details: pH 7.50, MICRODIALYSIS, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Details: referred to 'Heinemann, U.', (1991) 'Embo J.', 10, 35-43
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mMDNA solution1
220 mMsodium cacodylate1
350 mMmagnesium chloride1
440 %MPD12
520 mMsodium cacodylate12
650 mMmagnesium chloride12

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→8 Å / Num. all: 7209 / Num. obs: 4704 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 8 Å / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0385

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.75→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.174 3799
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 8 80 492
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_it2.823
X-RAY DIFFRACTIONn_sugar_angle_it4.285
X-RAY DIFFRACTIONn_phos_bond_it2.985
X-RAY DIFFRACTIONn_phos_angle_it4.055
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0160.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.040.04
X-RAY DIFFRACTIONn_phos_bond_d0.0450.04
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0640.06
X-RAY DIFFRACTIONn_plane_restr0.0250.03
X-RAY DIFFRACTIONn_chiral_restr0.0870.1
X-RAY DIFFRACTIONn_singtor_nbd0.1430.25
X-RAY DIFFRACTIONn_multtor_nbd0.20.25
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 8 Å / Num. reflection obs: 3799 / σ(F): 2 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

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