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- PDB-5ch0: Crystal structure of an A-form DNA duplex containing 5-hydroxylme... -

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Basic information

Entry
Database: PDB / ID: 5ch0
TitleCrystal structure of an A-form DNA duplex containing 5-hydroxylmethylcytidine
ComponentsDNA (5'-R(*G)-D(P*(UMS))-R(P*G)-D(P*T)-R(P*A)-D(P*(5HC))-R(P*AP*C)-3')
KeywordsDNA / A-form DNA duplex / 5hmC
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSheng, J.
CitationJournal: To Be Published
Title: Crystal structure of an A-form DNA duplex containing 5-hydroxylmethylcytidine
Authors: Sheng, J.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 20, 2021Group: Data collection / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _entity_poly.type / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-R(*G)-D(P*(UMS))-R(P*G)-D(P*T)-R(P*A)-D(P*(5HC))-R(P*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,5361
Polymers2,5361
Non-polymers00
Water66737
1
A: DNA (5'-R(*G)-D(P*(UMS))-R(P*G)-D(P*T)-R(P*A)-D(P*(5HC))-R(P*AP*C)-3')

A: DNA (5'-R(*G)-D(P*(UMS))-R(P*G)-D(P*T)-R(P*A)-D(P*(5HC))-R(P*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0712
Polymers5,0712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1930 Å2
ΔGint7 kcal/mol
Surface area2920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.050, 43.050, 23.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-137-

HOH

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Components

#1: DNA chain DNA (5'-R(*G)-D(P*(UMS))-R(P*G)-D(P*T)-R(P*A)-D(P*(5HC))-R(P*AP*C)-3')


Mass: 2535.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 46.33 % / Description: Tetragonal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% MPD, 40 mM Na cacodylate pH 7.0, 12 mM spermine tetra-HCl, 12mM KCl and 80 mM NaCl

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 4738 / % possible obs: 99.5 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 52.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 9.57 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z7I

1z7i


Resolution: 1.4→30.44 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 0.869 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20107 215 4.6 %RANDOM
Rwork0.18974 ---
obs0.19029 4496 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.767 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.4→30.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 164 0 37 201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021183
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6443280
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.232
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0283
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1540.260
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2710.2109
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0770.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7293262
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.24.5280
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.399→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.14 14 -
Rwork0.209 308 -
obs--96.12 %

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