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- PDB-5yze: Crystal structure of the [Co2+-(chromomycin A3)2]-d(CCG)3 complex -

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Basic information

Entry
Database: PDB / ID: 5yze
TitleCrystal structure of the [Co2+-(chromomycin A3)2]-d(CCG)3 complex
ComponentsDNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')
KeywordsANTIBIOTICS/DNA / Drug-DNA complex / Chromomycin A3 / CCG repeats / i-motif / flipout / DNA / ANTIBIOTICS-DNA complex
Function / homology: / Chem-CPH / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.87 Å
AuthorsHou, M.H. / Chen, Y.W. / Wu, P.C. / Satange, R.B.
CitationJournal: Int J Mol Sci / Year: 2018
Title: CoII(Chromomycin)2 Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex
Authors: Chen, Y.W. / Satange, R. / Wu, P.C. / Jhan, C.R. / Chang, C.K. / Chung, K.R. / Waring, M.J. / Lin, S.W. / Hsieh, L.C. / Hou, M.H.
History
DepositionDec 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_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.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Jan 20, 2021Group: Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity_poly / struct_conn
Item: _chem_comp.pdbx_synonyms / _entity_poly.type / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,11011
Polymers6,5902
Non-polymers2,5199
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-20 kcal/mol
Surface area4140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.401, 46.401, 73.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: -y,-x,-z+1/3
#5: -x+y,y,-z+2/3
#6: x,x-y,-z

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Components

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DNA chain , 1 types, 2 molecules AB

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


Mass: 3295.150 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, 82 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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.75mM DNA, 1.5mM Chro, 3mM Cobalt, 50mM Sodium Cacodylate (pH= 6.0), 1mM MgCl2, 1% MPD eqillibriated against 30% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.56418 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56418 Å / Relative weight: 1
ReflectionResolution: 1.87→27.2 Å / Num. obs: 7726 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 31.27 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 44.55
Reflection shellResolution: 1.87→1.94 Å / Rmerge(I) obs: 0.171 / Num. unique obs: 775 / Rsym value: 0.171

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Processing

Software
NameClassification
PHENIXrefinement
SHELXDEphasing
HKL-2000data scaling
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.87→27.18 Å / SU ML: 0.142 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 30.171
RfactorNum. reflection% reflection
Rfree0.252 354 4.593 %
Rwork0.194 --
obs0.196 7708 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.48 Å2
Refinement stepCycle: LAST / Resolution: 1.87→27.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 398 169 77 644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006622
X-RAY DIFFRACTIONf_angle_d1.008914
X-RAY DIFFRACTIONf_dihedral_angle_d26.219276
X-RAY DIFFRACTIONf_chiral_restr0.05120
X-RAY DIFFRACTIONf_plane_restr0.00726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8702-2.14070.24651060.18552420X-RAY DIFFRACTION100
2.1407-2.69670.2931200.23742442X-RAY DIFFRACTION100
2.6967-27.18660.23951280.18192492X-RAY DIFFRACTION100
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)
14.0819-0.0868-0.3239.57022.45695.44220.1027-0.1725-0.0314-0.1212-0.58461.33320.3643-0.44390.34190.2848-0.0020.01080.2422-0.02560.3881-5.604618.04527.7904
24.1510.26-0.64649.21411.79794.69530.26560.35660.11110.1964-0.51611.1762-0.1666-0.36740.36680.31990.0117-0.02250.233-0.02580.373-5.64158.72994.4588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )A1 - 11
2X-RAY DIFFRACTION2chain 'B' and (resid 12 through 22 )B12 - 22

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