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- PDB-253d: CRYSTAL STRUCTURE OF THE B-DNA NONAMER D(GCGTACGCG) WITH A NOVEL ... -

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Basic information

Entry
Database: PDB / ID: 253d
TitleCRYSTAL STRUCTURE OF THE B-DNA NONAMER D(GCGTACGCG) WITH A NOVEL D[G*(G.C)] BASE-TRIPLET INVOLVING THE MINOR GROOVE
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / BASE TRIPLET
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMooers, B.H.M. / Ho, P.S.
CitationJournal: To be Published / Year: 1996
Title: Crystal Structure of the B-DNA Nonamer d(GCGTACGCG) with a Novel d[G*(G.C)] Base-triplet Involving the Minor Groove
Authors: Mooers, B.H.M. / Ho, P.S.
History
DepositionMar 20, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 15, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,7812
Polymers2,7571
Non-polymers241
Water52229
1
A: DNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,5624
Polymers5,5142
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)38.915, 38.915, 33.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-10-

MG

21A-13-

HOH

31A-28-

HOH

41A-36-

HOH

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Components

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


Mass: 2756.811 Da / Num. of mol.: 1 / 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.: 29 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE11
6WATER12
7MPD12

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Data collection

Diffraction sourceSource: SEALED TUBE
DetectorType: SIEMENS P4 / Detector: DIFFRACTOMETER / Date: Aug 20, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→32 Å / Num. all: 1958 / Num. obs: 1126 / % possible obs: 76.43 % / Rmerge(I) obs: 0.042

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Processing

Software
NameClassification
X-PLORrefinement
XSCANSdata reduction
RefinementResolution: 2.2→8 Å / σ(F): 1
RfactorNum. reflection
Rfree0.2137 -
Rwork0.1931 -
obs0.1931 920
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 183 3 27 213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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