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- PDB-8asm: Cobalt(II) bound to a non-canonical quadruplex -

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Basic information

Entry
Database: PDB / ID: 8asm
TitleCobalt(II) bound to a non-canonical quadruplex
ComponentsDNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
KeywordsDNA
Function / homology: / COBALT HEXAMMINE(III) / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLambert, M.C. / Hall, J.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Citation
Journal: To Be Published
Title: Identifying metal-DNA binding sites, what is the best method to get transition metals into a crystal system?
Authors: Lambert, M.C. / Hall, J.P. / Brazier, J.A. / Cardin, C.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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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*AP*TP*GP*CP*T)-3')
B: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9898
Polymers4,2272
Non-polymers7626
Water93752
1
A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9898
Polymers4,2272
Non-polymers7626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
B: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules

B: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9898
Polymers4,2272
Non-polymers7626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)21.898, 58.659, 45.567
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-233-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DT / End label comp-ID: DT / Auth seq-ID: 1 - 7 / Label seq-ID: 1 - 7

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.99945803338, -0.0288444263618, 0.015863120145), (0.0288387166825, -0.999583904409, -0.000588614492466), (0.0158734978181, -0.000130823455496, 0.999873999538)Vector: - ...NCS oper: (Code: given
Matrix: (-0.99945803338, -0.0288444263618, 0.015863120145), (0.0288387166825, -0.999583904409, -0.000588614492466), (0.0158734978181, -0.000130823455496, 0.999873999538)
Vector: -22.1566343722, -8.39193062464, 0.191445602614)

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Components

#1: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')


Mass: 2113.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.75 Å3/Da / Density % sol: 29.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 2 ul 40 mM sodium cacodylate, 1 ul 80 mM hexammine (III) cobalt, 1 ul 10% MPD, 2 ul 800 mM potassium chloride, ul 30 mM sodium chloride, 2 ul 1 mM DNA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→18.71 Å / Num. obs: 3466 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 4.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.021 / Rrim(I) all: 0.047 / Net I/σ(I): 30.1
Reflection shellResolution: 1.7→1.75 Å / Num. unique obs: 294 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
CrysalisPro42.60adata collection
CrysalisPro42.60adata reduction
CrysalisPro42.60adata scaling
PHASER1.20.1_4487phasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MF5

1mf5


Resolution: 1.7→18.71 Å / SU ML: 0.084 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 18.3786
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1922 331 5.32 %
Rwork0.1782 5892 -
obs0.1789 3438 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 280 30 53 363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091336
X-RAY DIFFRACTIONf_angle_d0.9841538
X-RAY DIFFRACTIONf_chiral_restr0.059454
X-RAY DIFFRACTIONf_plane_restr0.00914
X-RAY DIFFRACTIONf_dihedral_angle_d32.5243132
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.550104831282 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-2.140.22131610.19592947X-RAY DIFFRACTION99.65
2.14-18.710.17381700.16732945X-RAY DIFFRACTION99.49
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.10743077099E-5-0.000608482643037-0.0002571951070910.005091098448260.002142432489570.001004538274230.003533989476810.004084281828150.008612227154350.00771921478657-0.0006226749797270.00448775568308-0.0200245302947-0.006109224444060.02258749943830.06833586694360.01854349229930.003461545000810.02927987285880.0139492431460.03182034031741.3142615504911.11330245946.5034430815
20.00744173732223-0.00503270211932-0.0004178533849040.00356406090196-0.0005723803514360.00348201672309-0.000460195870012-0.0031082685107-0.00362169717632-0.006039256640010.005249140085990.01189893068450.0106282595633-0.0006671927372310.03912223483150.014829043991-0.00505198833368-0.001754150917590.02533629074450.01454468040870.02217238637131.32545023222-2.5335697305816.300606378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )AA1 - 7
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 7 )BB1 - 7

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