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- PDB-158d: CRYSTALLOGRAPHIC ANALYSIS OF C-C-A-A-G-C-T-T-G-G AND ITS IMPLICAT... -

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Basic information

Entry
Database: PDB / ID: 158d
TitleCRYSTALLOGRAPHIC ANALYSIS OF C-C-A-A-G-C-T-T-G-G AND ITS IMPLICATIONS FOR BENDING IN B-DNA
ComponentsDNA (5'-D(*CP*CP*AP*AP*GP*CP*TP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsGrzeskowiak, K. / Goodsell, D.S. / Kaczor-Grzeskowiak, M. / Cascio, D. / Dickerson, R.E.
CitationJournal: Biochemistry / Year: 1993
Title: Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA.
Authors: Grzeskowiak, K. / Goodsell, D.S. / Kaczor-Grzeskowiak, M. / Cascio, D. / Dickerson, R.E.
History
DepositionFeb 3, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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.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.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: DNA (5'-D(*CP*CP*AP*AP*GP*CP*TP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*AP*GP*CP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1704
Polymers6,0902
Non-polymers802
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.080, 53.080, 34.320
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
11B-30-

HOH

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Components

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


Mass: 3045.004 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 7.5 / Details: pH 7.50, VAPOR DIFFUSION, temperature 278.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CA ACETATE11
4WATER12
5MPD12

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Data collection

DiffractionMean temperature: 278 K
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. all: 4165 / Num. obs: 4095 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 89 % / Observed criterion σ(F): 2 / Rmerge F obs: 0.0561

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.9→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.179 4095
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 15 62 481
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.0160.03
X-RAY DIFFRACTIONn_angle_d0.0340.04
X-RAY DIFFRACTIONn_plane_restr0.010.02
X-RAY DIFFRACTIONn_chiral_restr0.10.15

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