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

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Basic information

Entry
Database: PDB / ID: 3gsj
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 / homologyChem-R1C / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 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: 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_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_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.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_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

Downloads & links

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Assembly

Deposited unit
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)5,0695
Polymers3,6711
Non-polymers1,3984
Water1,13563
1
A: 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3'
hetero molecules

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)10,13810
Polymers7,3432
Non-polymers2,7958
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area1290 Å2
ΔGint-20 kcal/mol
Surface area5390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.020, 39.020, 57.420
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-2002-

R1C

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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.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Details: ORGANOMETALLIC
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 20 mM sodium cacodylate, 6 mM spermine, 4HCl, 40 mM KCl, 5% MPD, pH 7, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→28.7 Å / Num. obs: 4469 / % possible obs: 98.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.3 / % possible all: 97.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXDphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→27.59 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.081 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21251 198 4.5 %RANDOM
Rwork0.18328 ---
obs0.18471 4190 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.081 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 260 92 63 415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.021402
X-RAY DIFFRACTIONr_bond_other_d0.0030.02173
X-RAY DIFFRACTIONr_angle_refined_deg4.2813631
X-RAY DIFFRACTIONr_angle_other_deg1.4683409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1980.250
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.02234
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0282
X-RAY DIFFRACTIONr_nbd_refined0.20.245
X-RAY DIFFRACTIONr_nbd_other0.2490.2169
X-RAY DIFFRACTIONr_nbtor_refined0.2890.2165
X-RAY DIFFRACTIONr_nbtor_other0.1120.264
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3590.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it2.1253678
X-RAY DIFFRACTIONr_scangle_it3.214.5631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 17 -
Rwork0.377 292 -
obs--96.26 %

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