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- PDB-4fs6: Crystal structure of the Z-DNA hexamer CGCGCG at 500 mM CaCl2 -

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Basic information

Entry
Database: PDB / ID: 4fs6
TitleCrystal structure of the Z-DNA hexamer CGCGCG at 500 mM CaCl2
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / Ca2+ 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 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0828
Polymers1,8101
Non-polymers2717
Water73941
1
A: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,16316
Polymers3,6202
Non-polymers54314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1760 Å2
ΔGint-101 kcal/mol
Surface area2600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)18.461, 18.461, 71.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

21A-239-

HOH

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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.: 1 / Source method: obtained synthetically / Details: Chemical synthesis
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 293 K / Method: temperature control / pH: 7
Details: 2.0mM DNA, 20mM Na cacodylate, 30% 2-methyl-2,4-pentanediol, 500mM CaCl2, 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
Reflection twinOperator: -h,-k,l / Fraction: 0.31
ReflectionResolution: 1.3→36 Å / Num. all: 3879 / Num. obs: 3859 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 7.49 Å2 / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.3→1.47 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.051 / Num. unique all: 539 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→23.821 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.7962 / σ(F): 2.92 / Phase error: 25.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.23 168 4.38 %RANDOM
Rwork0.1895 ---
obs0.1951 3832 98.79 %-
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.397 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso max: 80.37 Å2 / Biso mean: 12.72 Å2 / Biso min: 1.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.5118 Å2-0 Å2-0 Å2
2--0.5118 Å20 Å2
3----1.0236 Å2
Refinement stepCycle: LAST / Resolution: 1.3→23.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 7 41 168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014134
X-RAY DIFFRACTIONf_angle_d1.862205
X-RAY DIFFRACTIONf_chiral_restr0.07323
X-RAY DIFFRACTIONf_plane_restr0.0066
X-RAY DIFFRACTIONf_dihedral_angle_d29.92956
LS refinement shellResolution: 1.3002→13.2757 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2323 168 -
Rwork0.1932 3654 -
all-3822 -
obs--94 %

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