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- PDB-1ue4: Crystal structure of d(GCGAAAGC) -

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Basic information

Entry
Database: PDB / ID: 1ue4
TitleCrystal structure of d(GCGAAAGC)
Components5'-D(*GP*CP*GP*AP*AP*AP*GP*C)-3'
KeywordsDNA / sheared G:A pair / bulge-in duplex / G:AxA:G crossing
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionMay 9, 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 1.3Oct 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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*CP*GP*AP*AP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4852
Polymers2,4611
Non-polymers241
Water1,18966
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)4,9704
Polymers4,9212
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)36.907, 36.907, 64.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.55 Å3/Da / Density % sol: 19.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium chloride, magnesium chloride, spermine 4HCl, 2-methyl-2,4-pentanediol, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium chloride11
2magnesium chloride11
3spermine 4HCl11
42-methyl-2,4-pentanediol11
5sodium cacodylate11
6sodium chloride12
7magnesium chloride12
8spermine 4HCl12
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mMprotein1drop
240 mMsodium cacodylate1droppH6.0
312 mM1drop
480 mM1dropNaCl
520 mM1dropMgCl2
610 %MPD1drop
725 %MPD1reservoir
81

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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: Oct 21, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→26 Å / Num. all: 3177 / Num. obs: 3175 / % possible obs: 99.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 7.6
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Num. measured all: 88780
Reflection shell
*PLUS
Highest resolution: 1.6 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: 1.65→15 Å / σ(F): 3
Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
RfactorNum. reflectionSelection details
Rfree0.2356 272 RANDOM
Rwork0.2089 --
all-2898 -
obs-2792 -
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 186 7 60 253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_bond_d0.004
LS refinement shellResolution: 1.65→1.71 Å /
RfactorNum. reflection
Rfree0.2355 30
Rwork0.1827 -
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.209
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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