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- PDB-2fza: Crystal structure of d(GCGGGAGC): the base-intercalated duplex -

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Basic information

Entry
Database: PDB / ID: 2fza
TitleCrystal structure of d(GCGGGAGC): the base-intercalated duplex
Components5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
KeywordsDNA / base-intercalated duplex / base-intercalated motif / sheared G:A pair / DNA hexaplex / deoxyribonucleic acid
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsKondo, J. / Ciengshin, T. / Juan, E.C.M. / Mitomi, K. / Takenaka, A.
CitationJournal: Nucleosides Nucleotides Nucleic Acids / Year: 2006
Title: Crystal structure of d(gcGXGAgc) with X=G: a mutation at X is possible to occur in a base-intercalated duplex for multiplex formation
Authors: Kondo, J. / Ciengshin, T. / Juan, E.C.M. / Sato, Y. / Mitomi, K. / Shimizu, S. / Takenaka, A.
History
DepositionFeb 9, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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

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Assembly

Deposited unit
A: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
B: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3389
Polymers5,1432
Non-polymers1957
Water362
1
A: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
B: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
hetero molecules

A: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
B: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
hetero molecules

A: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
B: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,01527
Polymers15,4296
Non-polymers58521
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)36.368, 36.368, 62.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-11-

CA

21A-13-

NA

31A-15-

NA

41B-12-

CA

51B-14-

NA

DetailsThe biological assembly is a DNA hexaplex generate from the three DNA duplex (X,Y,Z),(-Y,X-Y,Z) and (-X+Y,-X,Z).

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Components

#1: DNA chain 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'


Mass: 2571.538 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM sodium cacodylate, 10mM spermine tetrahydrochloride, 20mM calcium chloride, 100mM sodium chloride, 10%(v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2spermine tetrahydrochloride11
3calcium chloride11
4sodium chloride11
52-methyl-2,4-pentanediol11
6HOH11
7sodium cacodylate12
8calcium chloride12
9sodium chloride12
10HOH12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAC Science DIP-2040 / Detector: CCD / Date: Jun 3, 2003
RadiationMonochromator: ROTATED-INCLINED SI(111) DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.605→31.496 Å / Num. obs: 525 / % possible obs: 93.6 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 3.1
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value
3.6-3.7995.315.30.2932.5689450.293
3.79-4.0292.416.40.3492.2753460.349
4.02-4.391.415.70.193.8548350.19
4.3-4.6594.1150.1424.6661440.142
4.65-5.0992.715.80.1275523330.127
5.09-5.6994.414.10.0976.7508360.097
5.69-6.5795.213.20.1076.4436330.107
6.57-8.059412.50.1045.5338270.104
8.05-11.3892.612.80.15.5295230.1
11.38-31.594.78.70.0825.7148170.082

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→10 Å / FOM work R set: 0.831 / σ(F): 3
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D52, 57-64 (1996).
RfactorNum. reflection% reflectionSelection details
Rfree0.329 66 12.3 %RANDOM
Rwork0.294 ---
obs-458 85.6 %-
Solvent computationBsol: 300 Å2
Refinement stepCycle: LAST / Resolution: 3.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 7 2 343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.6-3.760.46970.3613744
3.76-3.940.79870.3315057
3.94-4.170.314110.2235061
4.17-4.470.23780.3044149
4.47-4.870.42380.2045563
4.87-5.470.52380.2435260
5.47-6.550.15870.2615360
6.55-100.298100.385464
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna_free.paramdna_free.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3brc_rep.parambrc.top
X-RAY DIFFRACTION4ion.paramion.top

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