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- PDB-210d: CRYSTAL AND MOLECULAR STRUCTURE OF A NEW Z-DNA CRYSTAL FORM: D[CG... -

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Basic information

Entry
Database: PDB / ID: 210d
TitleCRYSTAL AND MOLECULAR STRUCTURE OF A NEW Z-DNA CRYSTAL FORM: D[CGT(2-NH2-A)CG] AND ITS PLATINATED DERIVATIVE
ComponentsDNA (5'-D(*CP*GP*TP*(1AP)P*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.35 Å
AuthorsParkinson, G.N. / Arvantis, G.M. / Lessinger, L. / Ginell, S.L. / Jones, R. / Gaffney, B. / Berman, H.M.
CitationJournal: Biochemistry / Year: 1995
Title: Crystal and molecular structure of a new Z-DNA crystal form: d[CGT(2-NH2-A)CG] and its platinated derivative.
Authors: Parkinson, G.N. / Arvanitis, G.M. / Lessinger, L. / Ginell, S.L. / Jones, R. / Gaffney, B. / Berman, H.M.
History
DepositionJun 13, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Mar 22, 1996Provider: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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(*CP*GP*TP*(1AP)P*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0272
Polymers1,8241
Non-polymers2021
Water43224
1
A: DNA (5'-D(*CP*GP*TP*(1AP)P*CP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*GP*TP*(1AP)P*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0534
Polymers3,6482
Non-polymers4052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)25.247, 25.247, 39.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 1824.231 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.91 Å3/Da / Density meas: 1.45 Mg/m3 / Density % sol: 35.5 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4MGCL211
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %MPD1drop
210 mMspermine1drop
315 mM1dropMgCl2
430 mMsodium cacodylate1drop
52 mMd[CGTA'CG]1drop
620 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.35 Å / Num. all: 4487 / Num. obs: 3408 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 2.1 Å / Num. obs: 3408 / % possible obs: 94 % / Observed criterion σ(F): 4 / Num. measured all: 4487
Reflection shell
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 1.5 Å / % possible obs: 53 %

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.35→12 Å / σ(F): 4
RfactorNum. reflection% reflection
Rwork0.174 --
obs0.174 2957 74.7 %
Refinement stepCycle: LAST / Resolution: 1.35→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 123 15 24 162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.88
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
Refinement
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 12 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg9.2
X-RAY DIFFRACTIONx_improper_angle_deg1.12

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