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- PDB-1ub8: Crystal structure of d(GCGAAGC), bending duplex with a bulge-in r... -

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Basic information

Entry
Database: PDB / ID: 1ub8
TitleCrystal structure of d(GCGAAGC), bending duplex with a bulge-in residue
Components5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
KeywordsDNA / sheared G:A pair / bulge-in duplex / G:AxA:G crossing
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsSunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing.
Authors: Sunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K. / Takenaka, A.
History
DepositionMar 31, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
B: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
C: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
D: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
E: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
F: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,33515
Polymers12,8856
Non-polymers1,4509
Water5,477304
1
A: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
B: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7785
Polymers4,2952
Non-polymers4833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
D: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9396
Polymers4,2952
Non-polymers6444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
F: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6174
Polymers4,2952
Non-polymers3222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.675, 48.856, 63.761
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
5'-D(*GP*CP*GP*AP*AP*GP*C)-3'


Mass: 2147.437 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: chemically synthesized
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.21 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium cacodylate, sodium chloride, potassium chloride, hexaamminecobalt(III) chloride, MEGA-10, 2-methyl-2,4-pentanediol, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2sodium chloride11
3potassium chloride11
4hexaamminecobalt(III) chloride11
5MEGA-1011
62-methyl-2,4-pentanediol11
7sodium cacodylate12
8sodium chloride12
9potassium chloride12
Crystal grow
*PLUS
Temperature: 277 K / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.5 mMprotein1drop
220 mM1reservoirpH6.0NaCl
3140 mM1reservoirKCl
420 mM1reservoirCo(NH3)6Cl3
518 %MPD1reservoir
60.17 %n-decanoyl-N-methylglucamide1reservoir
740 mM1reservoir
81
91

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→24 Å / Num. all: 20712 / Num. obs: 20709 / % possible obs: 100 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.4
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Num. measured all: 328413
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→24 Å / σ(F): 3
RfactorNum. reflectionSelection details
Rfree0.2315 1999 RANDOM
Rwork0.1942 --
all-20662 -
obs-20173 -
Refinement stepCycle: LAST / Resolution: 1.6→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 63 304 1225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.7
X-RAY DIFFRACTIONc_bond_d0.003
LS refinement shellResolution: 1.6→1.66 Å /
RfactorNum. reflection
Rfree0.2721 195
Rwork0.2413 -
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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