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- PDB-6l76: Crystal structure of the Ni(II)(Chro)2-d(TTGGGCCGAA/TTCGGCCCAA) c... -

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Basic information

Entry
Database: PDB / ID: 6l76
TitleCrystal structure of the Ni(II)(Chro)2-d(TTGGGCCGAA/TTCGGCCCAA) complex at 2.94 angstrom resolution
Components
  • DNA (5'-D(*TP*TP*CP*GP*GP*CP*CP*CP*AP*A)-3')
  • DNA (5'-D(*TP*TP*GP*GP*GP*CP*CP*GP*AP*A)-3')
KeywordsDNA / Duplex DNA / GGGGCC motif / nucleotide flipping-out / Hoogsteen base pair
Function / homologyChem-CPH / NICKEL (II) ION / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsHou, M.H. / Jhan, C.R. / Satange, R.B. / Lin, S.M.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction.
Authors: Jhan, C.R. / Satange, R. / Wang, S.C. / Zeng, J.Y. / Horng, Y.C. / Jin, P. / Neidle, S. / Hou, M.H.
History
DepositionOct 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,27623
Polymers12,1804
Non-polymers5,09619
Water75742
1
A: DNA (5'-D(*TP*TP*GP*GP*GP*CP*CP*GP*AP*A)-3')
B: DNA (5'-D(*TP*TP*CP*GP*GP*CP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,60911
Polymers6,0902
Non-polymers2,5199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4 kcal/mol
Surface area3900 Å2
MethodPISA
2
C: DNA (5'-D(*TP*TP*CP*GP*GP*CP*CP*CP*AP*A)-3')
D: DNA (5'-D(*TP*TP*GP*GP*GP*CP*CP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,66712
Polymers6,0902
Non-polymers2,57710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-4 kcal/mol
Surface area3990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.718, 64.718, 246.578
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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DNA chain , 2 types, 4 molecules ADBC

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


Mass: 3085.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*TP*CP*GP*GP*CP*CP*CP*AP*A)-3')


Mass: 3004.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 8 molecules

#3: Polysaccharide
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H- ...2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate


Type: oligosaccharide / Mass: 318.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ad212m-1b_1-5_4*OCC/3=O][ad112m-1a_1-5_4*OC]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-2-deoxy-Fucp4Ac]{[(3+1)][a-D-2-deoxy-Fucp4Me]{}}LINUCSPDB-CARE
#4: Polysaccharide
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol- ...3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol


Type: oligosaccharide / Mass: 432.506 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[ad222m-1b_1-5][ad611m-1a_1-5_3*C_4*OCC/3=O]/1-1-2/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2,6-deoxy-Glcp]{[(3+1)][a-L-2,6-deoxy-Glcp4Ac]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 53 molecules

#5: Chemical
ChemComp-CPH / (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose / None


Mass: 420.410 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H24O9
#6: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 6.12 Å3/Da / Density % sol: 79.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1mM TTGGGCCGAA, 1 mM TTCGGCCCAA, 3 mM Chromomycin A3, 6 mM NiSO4, 2.5 mM Spermine,40 mM Sodium cacodylate (pH=7), 4 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.94→30 Å / Num. obs: 12146 / % possible obs: 98.6 % / Redundancy: 9.3 % / Biso Wilson estimate: 74.54 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.023 / Rrim(I) all: 0.071 / Χ2: 0.909 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.94-3.0410.40.5096690.9360.1620.5350.689100
3.04-3.1710.20.2356840.9890.0760.2480.805100
3.17-3.319.90.1516980.9950.050.1590.931100
3.31-3.499.80.1266980.9960.0420.1330.95100
3.49-3.79.60.1176950.9940.040.1241.066100
3.7-3.999.50.0927120.9970.0310.0971.074100
3.99-4.3990.0667070.9980.0230.071.05899.6
4.39-5.028.50.067220.9960.0220.0641.06699
5.02-6.328.50.0477300.9980.0170.050.8796.8
6.32-307.80.0337760.9990.0120.0350.57691.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VAQ

1vaq


Resolution: 2.94→25.511 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.87
RfactorNum. reflection% reflection
Rfree0.2762 1248 10.27 %
Rwork0.2346 --
obs0.2389 12146 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 214.51 Å2 / Biso mean: 93.8655 Å2 / Biso min: 61.48 Å2
Refinement stepCycle: final / Resolution: 2.94→25.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 787 339 52 1178
Biso mean--88.46 110.04 -
Num. residues----39
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131264
X-RAY DIFFRACTIONf_angle_d1.381843
X-RAY DIFFRACTIONf_chiral_restr0.578236
X-RAY DIFFRACTIONf_plane_restr0.00959
X-RAY DIFFRACTIONf_dihedral_angle_d29.415418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.94-3.05740.30861360.2875120799
3.0574-3.19630.26511380.22321219100
3.1963-3.36450.28441370.19661222100
3.3645-3.57480.22991420.20911232100
3.5748-3.84990.27991380.22341214100
3.8499-4.23580.24731410.21751220100
4.2358-4.84510.24931420.20711213100
4.8451-6.09050.28521400.2309119098
6.0905-25.510.32131340.2894118195
Refinement TLS params.Method: refined / Origin x: -26.1521 Å / Origin y: 6.1794 Å / Origin z: -14.636 Å
111213212223313233
T1.572 Å20.7793 Å20.1047 Å2-0.3068 Å20.2227 Å2--0.6463 Å2
L2.9085 °2-0.0884 °2-0.2765 °2-1.9851 °2-0.5325 °2--1.1217 °2
S0.63 Å °0.7639 Å °-0.2108 Å °0.1659 Å °-1.1268 Å °0.5923 Å °-1.0954 Å °0.1688 Å °0.0927 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 10
2X-RAY DIFFRACTION1allB11 - 20
3X-RAY DIFFRACTION1allE21 - 36
4X-RAY DIFFRACTION1allC1 - 9
5X-RAY DIFFRACTION1allD11 - 20
6X-RAY DIFFRACTION1allF21 - 36
7X-RAY DIFFRACTION1allG1 - 7
8X-RAY DIFFRACTION1allH8 - 59

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