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- PDB-1lu5: 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex... -

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Basic information

Entry
Database: PDB / ID: 1lu5
Title2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(ammine)(cyclohexylamine)}2+ Bound to a Dodecamer DNA Duplex
Components
  • 5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3'
  • 5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3'
KeywordsDNA / platinum-DNA complex
Function / homologyCIS-(AMMINE)(CYCLOHEXYLAMINE)PLATINUM(II) COMPLEX / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSilverman, A.P. / Bu, W. / Cohen, S.M. / Lippard, S.J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: 2.4-A Crystal Structure of the Asymmetric Platinum Complex {Pt(ammine)(cyclohexylamine)}2+ Bound to a Dodecamer DNA Duplex
Authors: Silverman, A.P. / Bu, W. / Cohen, S.M. / Lippard, S.J.
History
DepositionMay 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2012Group: Derived calculations
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,2766
Polymers14,6544
Non-polymers6232
Water84747
1
A: 5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3'
B: 5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6383
Polymers7,3272
Non-polymers3111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3'
D: 5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6383
Polymers7,3272
Non-polymers3111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.644, 35.638, 46.556
Angle α, β, γ (deg.)79.53, 83.02, 81.36
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 3565.316 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3'


Mass: 3761.468 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-LPT / CIS-(AMMINE)(CYCLOHEXYLAMINE)PLATINUM(II) COMPLEX


Mass: 311.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16N2Pt
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.78 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: spermine, sodium cacodylate, magnesium acetate, PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1spermine11
2sodium cacodylate11
3magnesium acetate11
4PEG 400011
Crystal grow
*PLUS
Temperature: 4. ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.2 mMprotein1drop
250 mM1reservoirpH6.5
312 mMspermine1reservoir
4120 mM1reservoirMg(OAc)2
515 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 7337 / % possible obs: 96.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.082 / Rsym value: 0.09 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.251 / Rsym value: 0.277 / % possible all: 96.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 42245 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 96.3 % / Rmerge(I) obs: 0.277

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AIO

1aio


Resolution: 2.4→50 Å / Num. parameters: 4163 / Num. restraintsaints: 4897 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2
Num. reflection% reflectionSelection details
all6604 --
Rfree-10 %random
obs-96.3 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1037
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 972 18 47 1037
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0003
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.004
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.075
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / Num. reflection obs: 5267 / Num. reflection Rfree: 565 / % reflection Rfree: 10 % / Rfactor all: 0.234 / Rfactor Rfree: 0.2495 / Rfactor Rwork: 0.2008
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.0003

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