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- PDB-6qt1: Radiation damage study on a 16mer DNA segment, structure at 0.48 ... -

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Basic information

Entry
Database: PDB / ID: 6qt1
TitleRadiation damage study on a 16mer DNA segment, structure at 0.48 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 / MOLECULAR REPLACEMENT / molecular replacement / 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 area1700 Å2
ΔGint-43 kcal/mol
Surface area6180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.823, 36.823, 161.926
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-211-

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


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: 2.16 Å3/Da / Density % sol: 42.97 %
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: 6.6-8.6

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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→31.29 Å / Num. obs: 3861 / % possible obs: 92.1 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.03 / Rrim(I) all: 0.053 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.5 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.850.7791890.6080.5490.95959
7.84-31.290.033640.9960.0240.04196.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SGS

1sgs


Resolution: 1.8→31.29 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.071 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. Water molecules found in close contacts because of two reasons. 1) Being a part of the coordination sphere of ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. Water molecules found in close contacts because of two reasons. 1) Being a part of the coordination sphere of Ca2+ ions, possibly in different configurations, could not be fully resolved. 2) Some water molecules are in contact with the phosphate moieties of the DNA, with some contact angles close to 90 degrees, suggesting these may be Mg2+ or Na+ ions - these were modelled as water molecules, because there were no sodium or magnesium salts present during purification and crystallization.
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 180 4.7 %RANDOM
Rwork0.2196 ---
obs0.2212 3671 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.25 Å2 / Biso mean: 49.345 Å2 / Biso min: 22.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.44 Å2-0 Å2
2--0.87 Å2-0 Å2
3----2.83 Å2
Refinement stepCycle: final / Resolution: 1.8→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 325 6 40 371
Biso mean--49.34 46.99 -
Num. residues----16
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.011364
X-RAY DIFFRACTIONr_bond_other_d0.0020.02181
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.172560
X-RAY DIFFRACTIONr_angle_other_deg1.7363429
X-RAY DIFFRACTIONr_chiral_restr0.0940.248
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.02192
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0280
LS refinement shellResolution: 1.801→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 11 -
Rwork0.311 161 -
all-172 -
obs--57.53 %
Refinement TLS params.Method: refined / Origin x: -10.8379 Å / Origin y: -20.1414 Å / Origin z: 54.1618 Å
111213212223313233
T0.0397 Å20.0243 Å2-0.0069 Å2-0.1913 Å2-0.0107 Å2--0.1114 Å2
L0.0591 °20.0884 °2-0.1182 °2-0.1379 °2-0.3482 °2--9.88 °2
S0.0217 Å °0.0265 Å °0.0707 Å °0.0136 Å °0.0534 Å °0.1129 Å °0.15 Å °-1.1831 Å °-0.0751 Å °

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