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- PDB-1f6c: CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE -

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Basic information

Entry
Database: PDB / ID: 1f6c
TitleCRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE
ComponentsDNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
KeywordsDNA / B-DNA / E-DNA / DOUBLE HELIX
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVargason, J.M. / Eichman, B.F. / Ho, P.S.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.
Authors: Vargason, J.M. / Eichman, B.F. / Ho, P.S.
History
DepositionJun 21, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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_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: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
B: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
D: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
E: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4567
Polymers9,0515
Non-polymers4052
Water28816
1
A: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')

A: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
2
B: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8233
Polymers3,6202
Non-polymers2021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
E: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8233
Polymers3,6202
Non-polymers2021
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.500, 71.500, 59.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

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


Mass: 1810.205 Da / Num. of mol.: 5 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4 Å3/Da / Density % sol: 69.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MGCL2, SPERMINE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2SPERMINE11
3MGCL211
4MGCL212
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.7 mMDNA1drop
225 mMsodium cacodylate1drop
30.8 mM1dropMgCl2
40.75 mMspermine-tetrahydrochloride1drop
515 %(v/v)MPD1reservoir
625 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→500 Å / Num. all: 4526 / Num. obs: 4526 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.7
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.395 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 32859
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: PARKINSON ET AL.
Details: ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 447 10.4 %RANDOM
Rwork0.226 ---
all0.233 4316 --
obs0.232 4304 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.9024 Å20 Å20 Å2
2---9.9024 Å20 Å2
3---19.8048 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 600 21 16 637
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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