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- PDB-4fs5: Crystal structure of the Z-DNA hexamer CGCGCG at 500 mM MgCl2 -

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Basic information

Entry
Database: PDB / ID: 4fs5
TitleCrystal structure of the Z-DNA hexamer CGCGCG at 500 mM MgCl2
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / Mg2+ binding
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsChatake, T. / Sunami, T.
CitationJournal: J.Inorg.Biochem. / Year: 2013
Title: Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl2
Authors: Chatake, T. / Sunami, T.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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(*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)4,00516
Polymers3,6202
Non-polymers38514
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-110 kcal/mol
Surface area2350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)18.593, 18.593, 72.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: Chemical synthesis
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 293 K / Method: temperature control / pH: 7
Details: 2.0mM DNA, 20mM Na cacodylate, 30% 2-methyl-2,4-pentainediol, 500mM MgCl2, pH 7.0, TEMPERATURE CONTROL, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2008
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→24.2 Å / Num. all: 6915 / Num. obs: 6868 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.12 / Num. unique all: 1006 / % possible all: 99

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Processing

Software
NameVersionClassification
BSSdata collection
AMoREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IO5

1io5


Resolution: 1.3→9.682 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7407 / SU ML: 0.2 / σ(F): 0.16 / Phase error: 32.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 322 4.72 %RABDOM
Rwork0.2109 ---
obs0.2133 6815 98.6 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.456 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso max: 30.13 Å2 / Biso mean: 14.8432 Å2 / Biso min: 7.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.5405 Å20 Å2-0 Å2
2---0.5405 Å20 Å2
3---1.0809 Å2
Refinement stepCycle: LAST / Resolution: 1.3→9.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 14 73 327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014268
X-RAY DIFFRACTIONf_angle_d1.849410
X-RAY DIFFRACTIONf_chiral_restr0.08246
X-RAY DIFFRACTIONf_plane_restr0.01512
X-RAY DIFFRACTIONf_dihedral_angle_d29.583112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3001-1.63660.27441620.20383235339798
1.6366-9.6820.26011600.21293258341899

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