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- PDB-2got: Crystal structure of d(GCGAACGC): two types of bulge-containing d... -

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Basic information

Entry
Database: PDB / ID: 2got
TitleCrystal structure of d(GCGAACGC): two types of bulge-containing duplexes
ComponentsDNA (5'-D(*DGP*(CBR)P*DGP*DAP*DAP*DCP*DGP*DC)-3')
KeywordsDNA / intra-duplex and inter-duplex hand-in-pocket motifs / bulge-containing duplex / base-intercalated duplex / single stranded DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.602 Å
AuthorsKondo, J. / Sunami, T. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch
Authors: Kondo, J. / Sunami, T. / Takenaka, A.
History
DepositionApr 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*DGP*(CBR)P*DGP*DAP*DAP*DCP*DGP*DC)-3')
B: DNA (5'-D(*DGP*(CBR)P*DGP*DAP*DAP*DCP*DGP*DC)-3')


Theoretical massNumber of molelcules
Total (without water)5,0312
Polymers5,0312
Non-polymers00
Water905
1
A: DNA (5'-D(*DGP*(CBR)P*DGP*DAP*DAP*DCP*DGP*DC)-3')

A: DNA (5'-D(*DGP*(CBR)P*DGP*DAP*DAP*DCP*DGP*DC)-3')


Theoretical massNumber of molelcules
Total (without water)5,0312
Polymers5,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
2
B: DNA (5'-D(*DGP*(CBR)P*DGP*DAP*DAP*DCP*DGP*DC)-3')

B: DNA (5'-D(*DGP*(CBR)P*DGP*DAP*DAP*DCP*DGP*DC)-3')


Theoretical massNumber of molelcules
Total (without water)5,0312
Polymers5,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)26.830, 26.830, 226.325
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain DNA (5'-D(*DGP*(CBR)P*DGP*DAP*DAP*DCP*DGP*DC)-3')


Mass: 2515.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.24 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40mM sodium cacodylate, 12mM spermine tetrahydrochloride, 80mM sodium chloride, 10%(v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2spermine tetrahydrochloride11
3sodium chloride11
42-methyl-2,4-pentanediol11
5HOH11
6sodium cacodylate12
7sodium chloride12
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1.00, 0.91955, 0.92010
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.919551
30.92011
ReflectionResolution: 2.602→25.147 Å / Num. obs: 1730 / % possible obs: 93 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.7412.70.2662.520741630.26664.9
2.74-2.9113.20.1594.128702180.15991.3
2.91-3.1116.90.1035.937172200.10399.8
3.11-3.36170.0558.840302370.05599.8
3.36-3.6818.20.0527.832801800.05299.7
3.68-4.11170.05211.331651860.05299.6
4.11-4.7515.90.04910.828711800.04999.5
4.75-5.8115.90.04711.223591480.04799.3
5.81-8.2214.40.04411.717691230.04498.9
8.22-25.1511.80.04111.6883750.04190.7

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
DPSdata reduction
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing
RefinementResolution: 2.602→25.147 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.914 / SU B: 12.436 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.27 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 158 9.2 %RANDOM
Rwork0.253 ---
obs0.254 1726 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.435 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20.68 Å20 Å2
2--1.36 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.602→25.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 378 0 5 383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021426
X-RAY DIFFRACTIONr_bond_other_d0.0040.02164
X-RAY DIFFRACTIONr_angle_refined_deg2.6543658
X-RAY DIFFRACTIONr_angle_other_deg2.0453422
X-RAY DIFFRACTIONr_chiral_restr0.1820.256
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02194
X-RAY DIFFRACTIONr_nbd_refined0.1710.280
X-RAY DIFFRACTIONr_nbd_other0.2210.2179
X-RAY DIFFRACTIONr_nbtor_other0.1120.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.420.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.29
X-RAY DIFFRACTIONr_scbond_it3.0613426
X-RAY DIFFRACTIONr_scangle_it4.8414.5658
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.807 3
Rwork0.461 71
obs-74
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna_free.param
X-RAY DIFFRACTION2brc.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water.param

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