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- PDB-1ick: LEFT-HANDED Z-DNA HEXAMER DUPLEX D(CGCGCG)2 -

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Basic information

Entry
Database: PDB / ID: 1ick
TitleLEFT-HANDED Z-DNA HEXAMER DUPLEX D(CGCGCG)2
Components5'-D(*CP*GP*CP*GP*CP*G)-3'
KeywordsDNA / left-handed Z-DNA oligomer
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2DCG model from PDB / Resolution: 0.95 Å
AuthorsDauter, Z. / Adamiak, D.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy.
Authors: Dauter, Z. / Adamiak, D.A.
History
DepositionApr 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_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: 5'-D(*CP*GP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8474
Polymers3,6202
Non-polymers2272
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.870, 31.550, 44.580
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 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.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30 mM cacodylate buffer, 15 mM MgCl2, 10 mM spermine, 5% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate buffer11
2MgCl211
3spermine11
4MPD11
5MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlDNA1drop
230 mMcacodylate1drop
315 mM1dropMgCl2
410 mMspermine1drop
55 %1drop
637.5 %MPD1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2000 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL CUT DOUBLE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 0.95→20 Å / Num. all: 16121 / Num. obs: 16121 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 4.2 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 58.7
Reflection shellResolution: 0.95→0.98 Å / Redundancy: 12 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 9.7 / Num. unique all: 1550 / Rsym value: 0.129 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 193475
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: 2DCG model from PDB
Starting model: 2DCG from PDB

2dcg


Resolution: 0.95→10 Å / Cross valid method: electron density maps / σ(F): -99 / σ(I): -99 / Stereochemistry target values: Parkinson et al.
Details: Anisotropic model for all atoms. The average rms error from the inversion of the lsq matrix is 0.01 Angstrom.
RfactorNum. reflection% reflection
obs0.0865 15782 98 %
all-16102 -
Refinement stepCycle: LAST / Resolution: 0.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 24 83 347
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_from_restr_planes0.157
X-RAY DIFFRACTIONs_approx_iso_adps0.081
LS refinement shellResolution: 0.95→10 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.016 --
Rfree-0 -
obs--98 %
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 15782 / Num. reflection obs: 16102 / Rfactor all: 0.0871
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.157
X-RAY DIFFRACTIONs_chiral_restr0.052

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