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- PDB-3p4j: Ultra-high resolution structure of d(CGCGCG)2 Z-DNA -

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Basic information

Entry
Database: PDB / ID: 3p4j
TitleUltra-high resolution structure of d(CGCGCG)2 Z-DNA
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.55 Å
AuthorsBrzezinski, K. / Brzuszkiewicz, A. / Dauter, M. / Kubicki, M. / Jaskolski, M. / Dauter, Z.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.
Authors: Brzezinski, K. / Brzuszkiewicz, A. / Dauter, M. / Kubicki, M. / Jaskolski, M. / Dauter, Z.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Refinement description
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*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)3,8233
Polymers3,6202
Non-polymers2021
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-10 kcal/mol
Surface area2590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.880, 31.420, 43.900
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 / Details: Synthetic construct
#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.: 128 / 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: 1.7 Å3/Da / Density % sol: 27.77 %
Crystal growTemperature: 293 K / pH: 7
Details: DNA water solution mixed 1:1 v/v with 10% MPD, 12 mM spermine tetra-HCl, 40 mM HEPES pH 7.0 and equilibrated against 35% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.5904
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2010 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI 111 DOUBLE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.5904 Å / Relative weight: 1
ReflectionResolution: 0.55→30 Å / Num. obs: 130650 / % possible obs: 84.5 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 2.45 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 16.7
Reflection shellResolution: 0.55→0.57 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.276 / % possible all: 53

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ICK

1ick


Resolution: 0.55→30 Å / Occupancy max: 1 / Occupancy min: 0.05 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: NONE
Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE AND NON-RESTRAINED ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.085 1724 -RANDOM
Rwork0.078 ---
all0.08 ---
obs0.078 130650 84.5 %-
Refinement stepCycle: LAST / Resolution: 0.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 14 128 382

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