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- PDB-1n5c: Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG -

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Basic information

Entry
Database: PDB / ID: 1n5c
TitleCrystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(EDC)P*GP*CP*G)-3'
KeywordsDNA / B form double helix / 3 / N4-etheno-2'-cytidine modification opposite G
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 1.79 Å
AuthorsFreisinger, E. / Fernandes, A. / Grollman, A.P. / Kisker, C.F.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystallographic Characterization of an Exocyclic DNA Adduct: 3,N4-etheno-2'-deoxycytidine in the Dodecamer 5'-CGCGAATT(ethenoC)GCG-3'
Authors: Freisinger, E. / Fernandes, A. / Grollman, A.P. / Kisker, C.F.
History
DepositionNov 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,7102
Polymers3,6871
Non-polymers231
Water1,31573
1
A: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(EDC)P*GP*CP*G)-3'
hetero molecules

A: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(EDC)P*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4214
Polymers7,3752
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+2/31
Unit cell
Length a, b, c (Å)26.723, 26.723, 101.544
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-1101-

NA

21A-1002-

HOH

31A-1042-

HOH

41A-1050-

HOH

51A-1056-

HOH

DetailsThe second part of the biological assembly/double helix is generated by the two fold axis: -x+y+1, y, -z+3/2.

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Components

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


Mass: 3687.414 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.34 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 277 K / pH: 7
Details: Drop: MPD, potassium chloride, spermine tetrahydrochloride, cacodylate; Reservoir: MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3spermine tetrahydrochloride11
4cacodylate11
5MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %(v/v)1drop
240 mMsodium cacodylate1droppH7.0
312 mM1drop
480 mM1dropKCl
535 %(v/v)1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2000
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 4113 / % possible obs: 99.4 % / Observed criterion σ(I): 5 / Redundancy: 4 % / Rsym value: 0.061 / Net I/σ(I): 22
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.187 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.79 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.061

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: NDB ENTRY BD0032

Resolution: 1.79→20 Å / Num. parameters: 1327 / Num. restraintsaints: 1445 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.219 200 5 %RANDOM
all0.164 3913 --
obs0.161 -99.6 %-
Solvent computationSolvent model: BABINET'S PRINCIPLE
Refine analyzeOccupancy sum hydrogen: 137 / Occupancy sum non hydrogen: 303.75
Refinement stepCycle: LAST / Resolution: 1.79→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 245 1 73 319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d2.6
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.007
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.065
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.143
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1612 / Rfactor Rfree: 0.2193 / Rfactor Rwork: 0.061
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.6

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