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- PDB-6qt6: Radiation damage study on a 16mer DNA segment, structure at 29.2 ... -

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Basic information

Entry
Database: PDB / ID: 6qt6
TitleRadiation damage study on a 16mer DNA segment, structure at 29.2 MGy dose
ComponentsDNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')
KeywordsDNA / radiation damage / global damage / specific damage
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsBugris, V. / Harmat, V. / Ferenc, G. / Brockhauser, S. / Carmichael, I. / Garman, E.F.
Funding support Germany, Hungary, 2items
OrganizationGrant numberCountry
European Molecular Biology OrganizationSTF_7639 Germany
European UnionVEKOP-2.3.3-15-2017-00018 Hungary
CitationJournal: J.Synchrotron Radiat. / Year: 2019
Title: Radiation-damage investigation of a DNA 16-mer.
Authors: Bugris, V. / Harmat, V. / Ferenc, G. / Brockhauser, S. / Carmichael, I. / Garman, E.F.
History
DepositionFeb 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1397
Polymers4,8981
Non-polymers2406
Water68538
1
A: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,27714
Polymers9,7962
Non-polymers48112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_435x-y-2/3,-y-4/3,-z+2/31
Buried area1710 Å2
ΔGint-42 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.965, 36.965, 162.571
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

CA

21A-102-

CA

31A-103-

CA

41A-213-

HOH

51A-227-

HOH

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Components

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


Mass: 4898.191 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Self complementary model DNA sequence derived from kB33 DNA segment. The present sequence is one nucleotide shorter than that of PDB structure 1SGS
Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 2 microliter 1.5 mM DNA solution (5mM HEPES pH 6.6) plus 2 microliter 10 mM HEPES pH 6.6 plus 4 microliter reservoir solution, against a reservoir of 1 ml 34% PEG200, 600 mM CaCl2 and 10 mM HEPES pH 8.6
PH range: 8.6-6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.8→31.43 Å / Num. obs: 3914 / % possible obs: 92.3 % / Redundancy: 3 % / CC1/2: 0.983 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.095 / Rrim(I) all: 0.167 / Net I/σ(I): 1.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) all% possible allCC1/2Mean I/σ(I) obs
1.8-1.852.6116.64819681.297143.06457.7
7.85-31.412.60.054640.0360.06595.70.995
2.48-2.613.22290.3970.73697.90.7652
2.36-2.483.22410.7681.42197.90.3651.5

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6QT1

6qt1


Resolution: 1.8→31.43 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.464 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.22
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The final model of the lowest dose dataset 6QT1 was further refined against the current dataset collected at higher dose.
RfactorNum. reflection% reflectionSelection details
Rfree0.3693 188 4.8 %RANDOM
Rwork0.2704 ---
obs0.2749 3721 91.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.02 Å2 / Biso mean: 57.745 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å20 Å2
3----2.58 Å2
Refinement stepCycle: final / Resolution: 1.8→31.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 325 6 40 371
Biso mean--76.69 56.7 -
Num. residues----16
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.011364
X-RAY DIFFRACTIONr_bond_other_d0.0020.02181
X-RAY DIFFRACTIONr_angle_refined_deg1.541.172560
X-RAY DIFFRACTIONr_angle_other_deg1.6543429
X-RAY DIFFRACTIONr_chiral_restr0.0930.248
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02192
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0280
LS refinement shellResolution: 1.801→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.627 12 -
Rwork0.596 175 -
all-187 -
obs--57.54 %

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