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- PDB-1i3t: MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATT(MO4)CGCG): THE WATS... -

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Basic information

Entry
Database: PDB / ID: 1i3t
TitleMOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATT(MO4)CGCG): THE WATSON-CRICK TYPE AND WOBBLE N4-METHOXYCYTIDINE/GUANOSINE BASE PAIRS IN B-DNA
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(C45)P*GP*CP*GP)-3'
KeywordsDNA / N4-METHOXYCYTOSINE / DAMAGED DNA / B-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHossain, M.T. / Hikima, T. / Chatake, T. / Masaru, T. / Sunami, T. / Ueno, Y. / Matsuda, A. / Takenaka, A.
CitationJournal: J.Biochem.(Tokyo) / Year: 2001
Title: Crystallographic studies on damaged DNAs: III. N(4)-methoxycytosine can form both Watson-Crick type and wobbled base pairs in a B-form duplex.
Authors: Hossain, M.T. / Chatake, T. / Hikima, T. / Tsunoda, M. / Sunami, T. / Ueno, Y. / Matsuda, A. / Takenaka, A.
History
DepositionFeb 16, 2001Deposition site: NDB / Processing site: RCSB
Revision 1.0Sep 14, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(C45)P*GP*CP*GP)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(C45)P*GP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4113
Polymers7,3872
Non-polymers241
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.182, 40.877, 63.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(C45)P*GP*CP*GP)-3'


Mass: 3693.418 Da / Num. of mol.: 2 / 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.: 110 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, magnesium acetate, spermine, sodium cacodylate. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277 K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium acetate11
2spermine11
3sodium cacodylate11
4MPD11
5MPD12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.25 mMDNA1drop
228 %(v/v)MPD1reservoir
336 mMmagnesium acetate1reservoir
49 mMspermine tetrahydrochloride1reservoir
520 mMsodium cacodylate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-18B11
SYNCHROTRONPhoton Factory BL-6B21
Detector
TypeIDDetectorDate
WEISSENBERG1DIFFRACTOMETERApr 18, 1999
WEISSENBERG2DIFFRACTOMETERDec 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 9068 / Num. obs: 9068 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.6→1.66 Å / Num. unique all: 759 / % possible all: 93.9
Reflection
*PLUS
Lowest resolution: 100 Å / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 93.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 355D

355d


Resolution: 1.6→10 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 936 10.5 %RANDOM
Rwork0.224 ---
all-8895 --
obs-8895 97.6 %-
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2---0.72 Å20 Å2
3----1.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 11 104 601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d1.41
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.429 74 8.9 %
Rwork0.376 759 -
obs--93.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10.5 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41
LS refinement shell
*PLUS
Rfactor Rfree: 0.429 / % reflection Rfree: 8.9 % / Rfactor Rwork: 0.376

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