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- PDB-1ue3: Crystal structure of d(GCGAAAGC) containing hexaamminecobalt -

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Basic information

Entry
Database: PDB / ID: 1ue3
TitleCrystal structure of d(GCGAAAGC) containing hexaamminecobalt
Components5'-D(*GP*CP*GP*AP*AP*AP*GP*C)-3'
KeywordsDNA / base-intercalated duplex / mini-hairpin structure / sheared G:A pair / zipper-like duplex
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure.
Authors: Sunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K.I. / Takenaka, A.
History
DepositionMay 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _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*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7065
Polymers2,4611
Non-polymers2454
Water72140
1
A: 5'-D(*GP*CP*GP*AP*AP*AP*GP*C)-3'
hetero molecules

A: 5'-D(*GP*CP*GP*AP*AP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,41210
Polymers4,9212
Non-polymers4908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)37.373, 37.373, 64.587
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-9-

CL

21A-768-

MG

31A-766-

NCO

41A-781-

HOH

51A-782-

HOH

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Components

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


Mass: 2460.644 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.97 Å3/Da / Density % sol: 37.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: magnesium chloride, spermine 4HCl, hexaamminecobalt(III) chloride, 2-methyl-2,4-pentanediol, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium chloride11
2spermine 4HCl11
3hexaamminecobalt(III) chloride11
42-methyl-2,4-pentanediol11
5sodium cacodylate11
6magnesium chloride12
7spermine 4HCl12
8hexaamminecobalt(III) chloride12
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.5 mMDNA1drop
218 mM1dropMgCl2
32.25 mMspermine 4HCl1drop
40.9 mM1dropCo(NH3)6Cl3
54.5 %MPD1drop
625 %MPD1reservoir
750 mMsodium cacodylate1droppH7.0
81

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→32 Å / Num. all: 1817 / Num. obs: 1817 / % possible obs: 100 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 6.2
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 1.9 / % possible all: 100
Reflection
*PLUS
Num. measured all: 102876
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UE2

1ue2


Resolution: 2.15→10 Å / σ(F): 3
Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
RfactorNum. reflectionSelection details
Rfree0.2389 146 RANDOM
Rwork0.2272 --
all-1661 -
obs-1538 -
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 186 22 28 236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
LS refinement shellResolution: 2.15→2.23 Å /
RfactorNum. reflection
Rfree0.2322 13
Rwork0.2282 -
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.4

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