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- PDB-4hp7: Trioxacarcin D517 as a product of guanine robbery from d(AACCGGTT) -

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Basic information

Entry
Database: PDB / ID: 4hp7
TitleTrioxacarcin D517 as a product of guanine robbery from d(AACCGGTT)
Components
  • (0) x Trioxacarcin A analogue, bound form
  • (1) x GUANINE
  • (2) x DIMETHYL SULFOXIDE
  • (3) x water
KeywordsANTIBIOTIC / Aminoglycosides / Anti-Bacterial Agents / Antitumor Agents / DNA
Function / homologyTrioxacarcin A analogue, bound form / GUANINE
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.09 Å
AuthorsSmaltz, D.J. / Magauer, T. / Proepper, K. / Dittrich, B. / Myers, A.G.
CitationJournal: TO BE PUBLISHED
Title: Trioxacarcin D517
Authors: Smaltz, D.J. / Magauer, T. / Proepper, K. / Dittrich, B. / Myers, A.G.
History
DepositionOct 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_conn
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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.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
Revision 1.2Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,48211
Polymers0
Non-polymers3,48211
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.086, 9.826, 35.093
Angle α, β, γ (deg.)90.00, 92.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Chemical
ChemComp-18Y / Trioxacarcin A analogue, bound form / (1S,2R,3aS,4S,13aS)-2-(dimethoxymethyl)-1,12-dihydroxy-7-methoxy-1,5-dimethyl-11-oxo-1,2,3a,4,8,9,10,11-octahydro-13aH-2,4-epoxyfuro[3,2-b]naphtho[2,3-h]chromen-13a-yl 4-C-acetyl-2,6-dideoxy-alpha-L-xylo-hexopyranoside


Mass: 660.662 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H40O14
Details: synthetic source form the laboratory of Andrew G. Myers
#2: Chemical
ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop
Details: The solution in the reservoir contained tri-ammonium citrate (pH 7.0) and 30% v/v DMSO. The DNA-drug solution 2.5 mM DNA (single-strand concentration), 2.8mM trioxacarcin A D5, VAPOR ...Details: The solution in the reservoir contained tri-ammonium citrate (pH 7.0) and 30% v/v DMSO. The DNA-drug solution 2.5 mM DNA (single-strand concentration), 2.8mM trioxacarcin A D5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.09→40 Å / Num. all: 7037 / % possible obs: 96.6 % / Redundancy: 3.14 % / Rmerge(I) obs: 0.0995 / Net I/σ(I): 6.28
Reflection shellResolution: 1.09→1.11 Å / Redundancy: 1.21 % / Rmerge(I) obs: 0.4339 / Mean I/σ(I) obs: 1.36 / % possible all: 52.9

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Processing

Software
NameVersionClassification
SHELXL2012refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 1.09→40 Å / Num. parameters: 2187 / Num. restraintsaints: 2331 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 1288 10 %RANDOM
obs0.1532 7037 96.6 %-
Refine analyzeNum. disordered residues: 3 / Occupancy sum non hydrogen: 247
Refinement stepCycle: LAST / Resolution: 1.09→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 242 7 249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0285
X-RAY DIFFRACTIONs_angle_d0.729
X-RAY DIFFRACTIONs_similar_dist0.159
X-RAY DIFFRACTIONs_from_restr_planes0.4909
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.12
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0263
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0

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