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- PDB-131d: THE LOW-TEMPERATURE CRYSTAL STRUCTURE OF THE PURE-SPERMINE FORM O... -

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Basic information

Entry
Database: PDB / ID: 131d
TitleTHE LOW-TEMPERATURE CRYSTAL STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA REVEALS BINDING OF A SPERMINE MOLECULE IN THE MINOR GROOVE
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1 Å
AuthorsBancroft, D. / Williams, L.D. / Rich, A. / Egli, M.
Citation
Journal: Biochemistry / Year: 1994
Title: The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove.
Authors: Bancroft, D. / Williams, L.D. / Rich, A. / Egli, M.
#1: Journal: Biochemistry / Year: 1991
Title: Structure of the Pure-Spermine Form of Z-DNA (Magnesium Free) at 1 Angstrom Resolution
Authors: Egli, M. / Williams, L.D. / Gao, Q. / Rich, A.
History
DepositionJun 18, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 15, 1993Provider: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0716
Polymers3,6202
Non-polymers4514
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.265, 30.690, 42.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.64 Å3/Da / Density % sol: 25.16 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2SPERMINE11
3WATER12
4MPD12
Crystal grow
*PLUS
pH: 7 / Details: Egli, M., (1991) Biochemistry, 30, 11388.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.4 mMDNA1dropsingle stranded
220 mMsodium cacodylate1drop
315 mMspermine tetrachloride1drop
420 %1reservoir

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Data collection

DiffractionMean temperature: 163 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1 Å / Num. all: 14081 / Num. obs: 9691 / Observed criterion σ(F): 2

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Processing

Software
NameVersionClassification
PROLSQ(MODIFIED BY G.J.QUIGLEY)refinement
MODIFIEDBY G.J.QUIGLEYrefinement
RefinementResolution: 1→5 Å / σ(F): 2 /
RfactorNum. reflection
obs0.18 9575
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL IONSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 30 62 332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1 Å / Lowest resolution: 5 Å / Num. reflection obs: 9575 / σ(F): 2 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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