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- PDB-1ihh: 2.4 ANGSTROM CRYSTAL STRUCTURE OF AN OXALIPLATIN 1,2-D(GPG) INTRA... -

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Basic information

Entry
Database: PDB / ID: 1ihh
Title2.4 ANGSTROM CRYSTAL STRUCTURE OF AN OXALIPLATIN 1,2-D(GPG) INTRASTRAND CROSS-LINK IN A DNA DODECAMER 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 / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / OXALIPLATIN / MODIFIED / DEOXYNUCLEIC ACID
Function / homology: / 1R,2R-DIAMINOCYCLOHEXANE / : / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsSpingler, B. / Whittington, D.A. / Lippard, S.J.
CitationJournal: Inorg.Chem. / Year: 2001
Title: 2.4 A crystal structure of an oxaliplatin 1,2-d(GpG) intrastrand cross-link in a DNA dodecamer duplex.
Authors: Spingler, B. / Whittington, D.A. / Lippard, S.J.
History
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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_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_label_seq_id / _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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7735
Polymers7,3272
Non-polymers4473
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.942, 51.246, 87.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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DNA chain , 2 types, 2 molecules AB

#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.: 1 / 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.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 15 molecules

#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#4: Chemical ChemComp-DNH / 1R,2R-DIAMINOCYCLOHEXANE


Mass: 114.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2
#5: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, SODIUM CACODYLATE, SPERMINE*4HCl, BACL2, ETHYL ACETATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2SODIUM CACODYLATE11
3SPERMINE*4HCl11
4BaCl211
5ETHYL ACETATE11
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.2 mMDNA1drop
22.5 %MPD1dropor 5%
320 mMsodium cacodylate1drop
46 mMspermine 4HCl1drop
510 mM1dropBaCl2
62.5 %ethyl acetate1drop
720 %MPD1reservoiror 30%
85 %ethyl acetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21731
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL9-110.970.97
SYNCHROTRONAPS 19-ID21.0721,1.0724,1.0277,1.1206
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEFeb 27, 2000
CUSTOM-MADE2CCDFeb 10, 2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.07211
31.07241
41.02771
51.12061
ReflectionResolution: 2.4→100 Å / Num. all: 61465 / Num. obs: 6296 / % possible obs: 93.7 % / Observed criterion σ(F): 4 / Redundancy: 9.76 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 18.9
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.5 / % possible all: 69
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 61465
Reflection shell
*PLUS
% possible obs: 69 %

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→100 Å / Num. parameters: 2052 / Num. restraintsaints: 2360 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.256 487 10 %RANDOM
Rwork0.209 ---
all-6296 --
obs-4935 93.7 %-
Displacement parametersBiso mean: 47.9 Å2
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 508
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 10 12 508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0.106
X-RAY DIFFRACTIONs_from_restr_planes0.001
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.006
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 4 / % reflection Rfree: 10 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.0005

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