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- PDB-5jw2: Crystal structure of mithramycin analogue MTM SA-Phe in complex w... -

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Basic information

Entry
Database: PDB / ID: 5jw2
TitleCrystal structure of mithramycin analogue MTM SA-Phe in complex with a 10-mer DNA AGGGATCCCT
ComponentsDNA (5'-D(*AP*GP*GP*GP*AP*TP*CP*CP*CP*T)-3')
KeywordsDNA/antibiotic / anti-cancer agent / DNA binding / natural product / transcription factor / Ewing sarcoma / DNA-antibiotic complex
Function / homologyPlicamycin, mithramycin analogue MTM SA-Phe / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsHou, C. / Rohr, J. / Tsodikov, O.V.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1.
Authors: Hou, C. / Weidenbach, S. / Cano, K.E. / Wang, Z. / Mitra, P. / Ivanov, D.N. / Rohr, J. / Tsodikov, O.V.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Mar 6, 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 / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,17011
Polymers6,0902
Non-polymers5,0809
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-160 kcal/mol
Surface area5840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.380, 49.380, 128.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Details1 complex of two MTM SA-Phe dimers bound to one double-stranded DNA oligomer

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Components

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


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-6O7 / Plicamycin, mithramycin analogue MTM SA-Phe / methyl (2S)-2-({(2S)-2-[(2R,3S)-3-{[(2S,4R,5R,6R)-4-{[(2S,4R,5S,6R)-4-{[(2S,4S,5R,6R)-4,5-dihydroxy-4,6-dimethyltetrahydro-2H-p yran-2-yl]oxy}-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-7-{[(2S,4 R,5R,6R)-4-{[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-5-hydroxy-6-methyltetrahydro-2H-pyran-2-y l]oxy}-5,10-dihydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-2-methoxyacetyl}amino)-3-phenylpropanoate (non-preferred name)


Mass: 1188.267 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C59H81NO24 / Comment: antineoplastic, antibiotic, inhibitor*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 6.42 Å3/Da / Density % sol: 80.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Incubated against 35% v/v 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 3055 / % possible obs: 99.6 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 25.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.889 / SU B: 21.357 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.455 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28824 156 4.9 %RANDOM
Rwork0.27932 ---
obs0.27973 3055 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.121 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å20 Å2
2---2.21 Å20 Å2
3---4.42 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 341 20 765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.015845
X-RAY DIFFRACTIONr_bond_other_d0.0050.02546
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9781246
X-RAY DIFFRACTIONr_angle_other_deg1.39431248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02390
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02136
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other0.1991.7071
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.531.23845
X-RAY DIFFRACTIONr_scbond_other0.5291.229846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9011.8381247
X-RAY DIFFRACTIONr_long_range_B_refined2.14612.7711179
X-RAY DIFFRACTIONr_long_range_B_other2.14512.7651180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 8 -
Rwork0.41 219 -
obs--100 %

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