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- PDB-6j0i: Structure of [Co2+-(Chromomycin A3)2]-d(TTGGCGAA)2 complex -

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Basic information

Entry
Database: PDB / ID: 6j0i
TitleStructure of [Co2+-(Chromomycin A3)2]-d(TTGGCGAA)2 complex
ComponentsDNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
KeywordsDNA/ANTIBIOTIC / Mismatch DNA / Chromomycin A3 / Drug-DNA complex / G:G mismatch / DNA-ANTIBIOTIC complex
Function / homology: / Chem-CRH / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSatange, R.B. / Chuang, C.Y. / Hou, M.H.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation.
Authors: Satange, R. / Chuang, C.Y. / Neidle, S. / Hou, M.H.
History
DepositionDec 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / 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 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.occupancy / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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*GP*GP*CP*GP*AP*A)-3')
B: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
C: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
D: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
E: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
F: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,04831
Polymers14,8006
Non-polymers7,24825
Water6,864381
1
A: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
B: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,33010
Polymers4,9332
Non-polymers2,3968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-4 kcal/mol
Surface area3210 Å2
MethodPISA
2
C: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
D: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,38911
Polymers4,9332
Non-polymers2,4559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-3 kcal/mol
Surface area3240 Å2
MethodPISA
3
E: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
F: DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,33010
Polymers4,9332
Non-polymers2,3968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-5 kcal/mol
Surface area3190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.826, 48.096, 96.725
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-258-

HOH

21C-261-

HOH

31E-220-

HOH

41F-242-

HOH

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Components

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DNA chain , 1 types, 6 molecules ABCDEF

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


Mass: 2466.641 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 12 molecules

#2: 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.: 6
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
#3: 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.: 6
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, 394 molecules

#4: Chemical
ChemComp-CRH / 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE


Mass: 388.411 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C21H24O7
#5: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 3.76 Å3/Da / Density % sol: 67.27 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 5mM Sodium Cacodylate (pH 7.3), 7mM MgCl2, 12mM Spermine, 4% PEG 400, 4% 1-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 12624 / % possible obs: 95.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.79 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.019 / Rrim(I) all: 0.047 / Χ2: 0.914 / Net I/σ(I): 21.7 / Num. measured all: 53369
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.512 / Num. unique obs: 549 / CC1/2: 0.996 / Rpim(I) all: 0.017 / Rrim(I) all: 0.037 / Χ2: 0.786 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VAQ

1vaq


Resolution: 2.5→16.12 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.79
RfactorNum. reflection% reflection
Rfree0.29 621 4.92 %
Rwork0.257 --
obs0.259 12624 84.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62 Å2 / Biso mean: 39.42 Å2 / Biso min: 14.33 Å2
Refinement stepCycle: final / Resolution: 2.5→16.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 984 505 384 1873
Biso mean--43.02 34.69 -
Num. residues----48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.496-2.7460.48491070.38292080218759
2.746-3.14080.35661870.3143422360996
3.1408-3.94750.29311770.237435673744100
3.9475-16.12120.22061500.2252934308482

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