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- PDB-5jvw: Crystal structure of mithramycin analogue MTM SA-Trp in complex w... -

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Basic information

Entry
Database: PDB / ID: 5jvw
TitleCrystal structure of mithramycin analogue MTM SA-Trp in complex with a 10-mer DNA AGAGGCCTCT.
ComponentsDNA (5'-D(*AP*GP*AP*GP*GP*CP*CP*TP*CP*T)-3')
Keywordsdna/antibiotic / anti-cancer agent / Ewing sarcoma / transcription factor / minor groove / DNA binding / dna-antibiotic complex
Function / homologyPlicamycin, mithramycin analogue MTM SA-Trp / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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

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


Theoretical massNumber of molelcules
Total (without water)18,10028
Polymers12,1804
Non-polymers5,92024
Water3,783210
1
A: DNA (5'-D(*AP*GP*AP*GP*GP*CP*CP*TP*CP*T)-3')
B: DNA (5'-D(*AP*GP*AP*GP*GP*CP*CP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,98312
Polymers6,0902
Non-polymers2,89310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: DNA (5'-D(*AP*GP*AP*GP*GP*CP*CP*TP*CP*T)-3')
D: DNA (5'-D(*AP*GP*AP*GP*GP*CP*CP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,11716
Polymers6,0902
Non-polymers3,02714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.567, 50.658, 92.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details1 complex of MTM SA-Trp with double-stranded DNA

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Components

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


Mass: 3045.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-6O6 / Plicamycin, mithramycin analogue MTM SA-Trp / 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-pyran-2-yl]oxy}-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-7-{[(2S,4R,5R,6R)-4-{[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-5,10-dihydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-2-methoxyacetyl}amino)-3-(1H-indol-3-yl)propanoate (non-preferred name)


Mass: 1227.303 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C61H82N2O24
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Incubation 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: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10439 / % possible obs: 95.8 % / Observed criterion σ(F): 1.74 / Redundancy: 3.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.135 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26713 574 5.2 %RANDOM
Rwork0.21869 ---
obs0.22118 10435 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.282 Å2
Baniso -1Baniso -2Baniso -3
1-3.03 Å20 Å20 Å2
2---1.32 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 807 368 210 1385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0141342
X-RAY DIFFRACTIONr_bond_other_d0.0130.02810
X-RAY DIFFRACTIONr_angle_refined_deg3.181.7081971
X-RAY DIFFRACTIONr_angle_other_deg1.78231779
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_restr0.1210.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02632
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02228
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_other0.0221.5271
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8031.6251342
X-RAY DIFFRACTIONr_scbond_other1.8021.6241343
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9682.4221976
X-RAY DIFFRACTIONr_long_range_B_refined3.35817.1512048
X-RAY DIFFRACTIONr_long_range_B_other3.23217.0672013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 34 -
Rwork0.257 752 -
obs--94.02 %

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