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- PDB-454d: INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTIO... -

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Basic information

Entry
Database: PDB / ID: 454d
TitleINTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3'
Components5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
KeywordsDNA / METALLOINTERCALATOR / INTERCALATION / MAJOR GROOVE RECOGNITION / PHOTOEXCITABLE
Function / homologyChem-RHM / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.2 Å
AuthorsKielkopf, C.L. / Erkkila, K.E. / Hudson, B.P. / Barton, J.K. / Rees, D.C.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of a photoactive rhodium complex intercalated into DNA.
Authors: Kielkopf, C.L. / Erkkila, K.E. / Hudson, B.P. / Barton, J.K. / Rees, D.C.
History
DepositionMar 3, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
B: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
C: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
D: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
E: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
F: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
G: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
H: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
I: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
J: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,77715
Polymers25,38510
Non-polymers2,3925
Water6,738374
1
A: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
B: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5553
Polymers5,0772
Non-polymers4781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
D: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5553
Polymers5,0772
Non-polymers4781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
F: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5553
Polymers5,0772
Non-polymers4781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
H: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5553
Polymers5,0772
Non-polymers4781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
J: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5553
Polymers5,0772
Non-polymers4781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.740, 23.980, 96.520
Angle α, β, γ (deg.)90.00, 93.24, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-342-

HOH

21E-281-

HOH

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Components

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


Mass: 2538.487 Da / Num. of mol.: 10 / Source method: obtained synthetically
#2: Chemical
ChemComp-RHM / DELTA-ALPHA-RH[2R,9R-DIAMINO-4,7-DIAZADECANE]9,10-PHENANTHRENEQUINONE DIIMINE / RH(ME2TRIEN)PHI


Mass: 478.395 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H27N6Rh
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MPD, CALCIUM ACETATE, SODIUM CACODYLATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP at 277 K, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1CALCIUM ACETATE11
2SODIUM CACODYLATE11
3MPD11
4MPD12
Crystal
*PLUS
Density % sol: 43.1 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMoligonucleotide1dropdouble strand
21.7 mMRh(Me2trien)phi3+1drop
350 mMcalcium acetate1drop
45 mMsodium cacodylate1drop
510 %MPD1drop
620 %MPD1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSSRL BL9-120.98
Detector
TypeIDDetector
RIGAKU RAXIS IV1IMAGE PLATE
MARRESEARCH2IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.981
ReflectionResolution: 1.2→17 Å / Num. all: 122830 / Num. obs: 122830 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 25
Reflection shellResolution: 1.2→1.3 Å / Rmerge(I) obs: 0.278 / % possible all: 88.2
Reflection
*PLUS
Num. measured all: 360925
Reflection shell
*PLUS
% possible obs: 88.2 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
SOLVEphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS
Starting model: INITIAL MODEL OBTAINED BY SIRAS WITH 10 IODINE POSITIONS

Resolution: 1.2→17 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 6141 5 %RANDOM
Rwork0.17 ---
obs0.17 122830 92.5 %-
all-122830 --
Refinement stepCycle: LAST / Resolution: 1.2→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1658 145 374 2177
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 17 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d1.2

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