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- PDB-1uhy: Crystal structure of d(GCGATAGC): the base-intercalated duplex -

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Basic information

Entry
Database: PDB / ID: 1uhy
TitleCrystal structure of d(GCGATAGC): the base-intercalated duplex
Components5'-D(*GP*(CBR)P*GP*AP*TP*AP*GP*C)-3'
KeywordsDNA / base-intercalated duplex / base-intercalated motif / sheared G:A pair / Deoxyribonucleic acid
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKondo, J. / Umeda, S.I. / Fujita, K. / Sunami, T. / Takenaka, A.
CitationJournal: J.Synchrotron Radiat. / Year: 2004
Title: X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue.
Authors: Kondo, J. / Umeda, S.I. / Fujita, K. / Sunami, T. / Takenaka, A.
History
DepositionJul 13, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 22, 2014Group: Derived calculations
Revision 1.4Dec 27, 2023Group: 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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*AP*TP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,9115
Polymers2,5311
Non-polymers3814
Water1,63991
1
A: 5'-D(*GP*(CBR)P*GP*AP*TP*AP*GP*C)-3'
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)17,46730
Polymers15,1836
Non-polymers2,28424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Unit cell
Length a, b, c (Å)37.000, 37.000, 65.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-103-

CL

21A-100-

NCO

31A-101-

NCO

41A-13-

HOH

51A-45-

HOH

61A-47-

HOH

71A-52-

HOH

81A-55-

HOH

91A-84-

HOH

101A-85-

HOH

111A-86-

HOH

121A-90-

HOH

131A-95-

HOH

141A-96-

HOH

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Components

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


Mass: 2530.526 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.7 Å3/Da / Density % sol: 27.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2-methyl-2,4-pentandiol, hexamine cobalt chloride, sodium chloride, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
12-methyl-2,4-pentandiol11
2hexamine cobalt chloride11
3magnesium chloride11
4sodium cacodylate11
5hexamine cobalt chloride12
6magnesium chloride12
7sodium cacodylate12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.5 mMDNA1drop
250 mMsodium cacodylate1reservoirpH7.0
32 mMhexamine cobalt chloride1reservoir
4100 mM1reservoirNaCl
510 %(v/v)MPD1reservoir
61
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD / Date: May 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→65.3 Å / Num. all: 2991 / Num. obs: 2919 / % possible obs: 89.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 4.7
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3 / % possible all: 83.5
Reflection
*PLUS
Lowest resolution: 65 Å / Num. measured all: 223225
Reflection shell
*PLUS
% possible obs: 83.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→22.87 Å / Cross valid method: THROUGHOUT / σ(F): 3
Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
RfactorNum. reflection% reflectionSelection details
Rfree0.239 250 -RANDOM
Rwork0.224 ---
all-3255 --
obs-2707 83.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.286 Å2-1.564 Å20 Å2
2---3.286 Å20 Å2
3---6.573 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.7→22.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 164 16 91 271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.7→1.78 Å /
RfactorNum. reflection
Rfree0.298 26
Rwork0.213 -
Refinement
*PLUS
Lowest resolution: 65 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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