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- PDB-3gsk: A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch -

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Basic information

Entry
Database: PDB / ID: 3gsk
TitleA Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch
Components5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3'
KeywordsDNA / DNA MISMATCH / METALLOINTERCALATOR / DNA RECOGNITION
Function / homologyCACODYLATE ION / Chem-R1C / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZeglis, B.M. / Pierre, V.C. / Kaiser, J.T. / Barton, J.K.
CitationJournal: Biochemistry / Year: 2009
Title: A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch: general architecture of the metalloinsertion binding mode
Authors: Zeglis, B.M. / Pierre, V.C. / Kaiser, J.T. / Barton, J.K.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Mar 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
B: 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3'
A: 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8195
Polymers7,3432
Non-polymers1,4763
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.337, 48.337, 69.505
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 3671.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA
#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.: 2 / Source method: obtained synthetically / Formula: C38H26N6Rh / Details: ORGANOMETALLIC
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 20 mM sodium cacodylate, 6 mM spermine, 4HCl,40 mM NaCl, 5% 2-methyl-2,4-pentanediol, pH 7, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.0046 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0046 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. obs: 22677 / % possible obs: 99.5 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 26.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXDphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→20.271 Å / SU ML: 0.3 / σ(F): 1.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 1131 4.99 %
Rwork0.1838 --
obs0.1859 22677 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.07 Å2 / ksol: 0.429 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→20.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 488 95 89 672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.67290.31261280.25462541X-RAY DIFFRACTION89
1.6729-1.7610.29591480.21792554X-RAY DIFFRACTION91
1.761-1.87130.22291420.18922627X-RAY DIFFRACTION92
1.8713-2.01560.26821380.18782690X-RAY DIFFRACTION93
2.0156-2.21830.24221300.19092685X-RAY DIFFRACTION96
2.2183-2.53870.22021650.17382791X-RAY DIFFRACTION98
2.5387-3.19650.2721500.18812798X-RAY DIFFRACTION99
3.1965-20.27230.18211300.17112860X-RAY DIFFRACTION100

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