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- PDB-5xew: Crystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex -

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Basic information

Entry
Database: PDB / ID: 5xew
TitleCrystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex
ComponentsDNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')
KeywordsDNA/ANTIBIOTIC / Trinucleotide repeats / neurological disease / induced fit recognition / metal binding ligand / consecutive bases flip-out / DNA deformation / molecular diagnostics / DNA-ANTIBIOTIC complex
Function / homologyChem-CPH / NICKEL (II) ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.751 Å
AuthorsTseng, W.H. / Wu, P.C. / Hou, M.H.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation
Authors: Tseng, W.H. / Chang, C.K. / Wu, P.C. / Hu, N.J. / Lee, G.H. / Tzeng, C.C. / Neidle, S. / Hou, M.H.
History
DepositionApr 6, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 21, 2017ID: 5ERZ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.title
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: diffrn_source / struct_ref_seq
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq.db_align_end
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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


Theoretical massNumber of molelcules
Total (without water)10,34411
Polymers7,8252
Non-polymers2,5199
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint42 kcal/mol
Surface area3900 Å2
Unit cell
Length a, b, c (Å)48.291, 48.291, 83.356
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-211-

HOH

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Components

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DNA chain , 1 types, 2 molecules AB

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


Mass: 3912.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 4 molecules

#2: 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.: 2
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
#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.: 2
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

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Non-polymers , 3 types, 94 molecules

#4: 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.: 2 / Source method: obtained synthetically / Formula: C21H24O9
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsThe force field of Chro unit used in the refinement of NiII(Chro)2-DNA complex structure was ...The force field of Chro unit used in the refinement of NiII(Chro)2-DNA complex structure was generated using the atomic resolution crystal structure of NiII(Chro)2.

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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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0 mM single stranded-DNA, 2.0 mM Chromomycin A3, 4mM NiSO4 6H2O, 50 mM sodium-cacodylate buffer, 5 mM MgCl2, 1 mM spermine, 3 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.45104,1.48491,1.48582
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.451041
21.484911
31.485821
ReflectionResolution: 1.75→30 Å / Num. obs: 21692 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 30.69 Å2 / Rmerge(I) obs: 0.05 / Χ2: 2.733 / Net I/σ(I): 28.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.75-1.816.10.3641.038196.5
1.81-1.898.90.2351.0781100
1.89-1.9710.40.1631.1991100
1.97-2.0710.70.1191.311100
2.07-2.210.70.0971.641100
2.2-2.3710.90.0781.9931100
2.37-2.6110.90.0762.821100
2.61-2.9910.70.0822.8461100
2.99-3.7710.70.0444.0741100
3.77-3010.40.0417.942199.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data processing
HKL-2000data scaling
SHELXphasing
PHENIX1.10.1-2155refinement
RefinementMethod to determine structure: MAD / Resolution: 1.751→23.192 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.95
RfactorNum. reflection% reflection
Rfree0.2379 2186 10.08 %
Rwork0.2071 --
obs0.2103 21692 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.53 Å2 / Biso mean: 39.6775 Å2 / Biso min: 20.71 Å2
Refinement stepCycle: final / Resolution: 1.751→23.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 368 247 89 704
Biso mean--40.82 42.77 -
Num. residues----20
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007714
X-RAY DIFFRACTIONf_angle_d1.0881056
X-RAY DIFFRACTIONf_chiral_restr0.055136
X-RAY DIFFRACTIONf_plane_restr0.0130
X-RAY DIFFRACTIONf_dihedral_angle_d27.056316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7508-1.78890.2631270.29191084121187
1.7889-1.83050.29931290.24511183131299
1.8305-1.87630.25751440.227212541398100
1.8763-1.9270.23421440.217712401384100
1.927-1.98360.26181260.190112101336100
1.9836-2.04760.28881480.207612381386100
2.0476-2.12080.21641380.200912341372100
2.1208-2.20560.3361340.250312301364100
2.2056-2.30590.27451320.221812381370100
2.3059-2.42740.2421360.249812081344100
2.4274-2.57920.28871360.234912331369100
2.5792-2.77810.32351260.266412441370100
2.7781-3.05710.25361380.269512431381100
3.0571-3.49820.23281460.193512111357100
3.4982-4.40240.20361450.176712501395100
4.4024-23.19410.20031370.17121206134399

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