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- PDB-1i1p: REFINEMENT INCLUDING EXPERIMENTAL MAD PHASES ALLOWS AN EXHAUSTIVE... -

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Basic information

Entry
Database: PDB / ID: 1i1p
TitleREFINEMENT INCLUDING EXPERIMENTAL MAD PHASES ALLOWS AN EXHAUSTIVE STUDY OF ORDERED SOLVENT MOLECULES FOR A PLATINATED DECANUCLEOTIDE
Components
  • 5'-D(*CP*CP*TP*CP*GP*CP*TP*CP*TP*C)-3'
  • 5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3'
KeywordsDNA / ANTITUMOR DRUG / CIS-DDP / INTERSTRAND CROSS-LINK / DEOXYRIBONUCLEIC ACID / SPERMINE
Function / homologyCisplatin / SPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å
AuthorsCoste, F. / Shepard, W. / Zelwer, C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Description of ordered solvent molecules in a platinated decanucleotide duplex refined at 1.6A resolution against experimental MAD phases.
Authors: Coste, F. / Shepard, W. / Zelwer, C.
#1: Journal: Nucleic Acids Res. / Year: 1999
Title: Crystal Structure of a Double-Stranded DNA Containing A Cisplatin Interstrand Cross-Link At 1.63 Angstrom Resolution: Hydration At The Platinated Site
Authors: Coste, F. / Malinge, J.M. / Serre, L. / Shepard, W. / Roth, M. / Leng, M. / Zelwer, C.
History
DepositionFeb 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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*GP*CP*TP*CP*TP*C)-3'
B: 5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5934
Polymers6,0912
Non-polymers5022
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.890, 29.980, 46.570
Angle α, β, γ (deg.)90.00, 95.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 2931.917 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3'


Mass: 3159.079 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum / Cisplatin


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#4: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: sodium cacodylate, NaCl, KCl, spermine, MPD, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2NaClSodium chloride11
3KCl11
4spermine11
5MPD11
6sodium cacodylate12
7NaClSodium chloride12
8KCl12
9MPD12
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.0825 mMDNA molecule1drop
220 mMsodium cacodylate1droppH6.0
35 mM1dropNaCl
430 mM1dropKCl
52.5 mMspermine1drop
62 %(v/v)MPD1drop
72.5 %MPD1reservoir
81
91

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 1.0906,1.0718,1.0711,1.0301
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.09061
21.07181
31.07111
41.03011
ReflectionResolution: 1.63→20 Å / Num. all: 7353 / Num. obs: 7333 / % possible obs: 93.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 14
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / % possible all: 97
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.63→20 Å / Stereochemistry target values: Hendrikson & Konnert
RfactorNum. reflectionSelection details
Rfree0.188 340 RANDOM
Rwork0.159 --
all-7353 -
obs-7322 -
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 15 135 554
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.1883 / Rfactor Rwork: 0.1585
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_d0.026

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