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- PDB-2o1i: RH(BPY)2CHRYSI complexed to mismatched DNA -

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Basic information

Entry
Database: PDB / ID: 2o1i
TitleRH(BPY)2CHRYSI complexed to mismatched DNA
Components5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3'
KeywordsDNA / DNA mismatch / metallointercalator / DNA recognition
Function / homologyChem-R1C / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.1 Å
AuthorsPierre, V.C. / Kaiser, J.T. / Barton, J.K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator.
Authors: Pierre, V.C. / Kaiser, J.T. / Barton, J.K.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6564
Polymers3,6471
Non-polymers2,0093
Water1,35175
1
A: 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)11,3128
Polymers7,2952
Non-polymers4,0176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)38.740, 38.740, 57.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1001-

R1C

21A-2013-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis y,x,-z.

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Components

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


Mass: 3647.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase synthesis
#2: Chemical ChemComp-R1C / bis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)[chrysene-5,6-diiminato(2-)-kappa~2~N,N']rhodium(4+) / DELTA-Rhodium(III)- bis-(2,2'-bipyridyl)-5,6-chrysenequinone diimine


Mass: 669.559 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H26N6Rh
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: SrCl2 40mM, MgCl2 10mM, Na-cacodylate 20mM, spermine-4HCl 6mM, MPD 5%(v/v)equilibrated against 35% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1SrCl211
2MgCl211
3Na-cacodylate11
4spermine-4HCl11
5MPD11
6HOH11
7SrCl212
8MgCl212
9Na-cacodylate12
10MPD12
11HOH12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSSRL BL11-121.03317
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEMay 5, 2006
ADSC QUANTUM 3152CCDMay 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.033171
ReflectionResolution: 1.1→24 Å / Num. obs: 17269 / % possible obs: 94 % / Redundancy: 8.7 % / Biso Wilson estimate: 14.85 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 13.4
Reflection shellResolution: 1.07→1.14 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.015 / Mean I/σ(I) obs: 0.9 / Rsym value: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
Blu-Icedata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: AB INITIO / Highest resolution: 1.1 Å / Num. parameters: 4070 / Num. restraintsaints: 5578 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.204 --RANDOM
all0.1515 ---
obs-17269 94 %-
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 178 / Occupancy sum non hydrogen: 384
Refinement stepCycle: LAST / Highest resolution: 1.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 242 135 75 452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.024
X-RAY DIFFRACTIONs_angle_d0.041
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0135
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.109

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