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- PDB-1em0: COMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN -

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Basic information

Entry
Database: PDB / ID: 1em0
TitleCOMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN
ComponentsDNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
KeywordsDNA / PORPHYRIN / RUFFLING / DNA DISTORTION / GROOVE BINDING
Function / homologyTETRA[N-METHYL-PYRIDYL] PORPHYRIN-NICKEL / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.9 Å
AuthorsNeidle, S. / Sanderson, M. / Bennett, M. / Krah, A. / Wien, F. / Garman, E. / McKenna, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: A DNA-porphyrin minor-groove complex at atomic resolution: the structural consequences of porphyrin ruffling.
Authors: Bennett, M. / Krah, A. / Wien, F. / Garman, E. / McKenna, R. / Sanderson, M. / Neidle, S.
History
DepositionMar 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 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 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.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: DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
B: DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
C: DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
D: DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0728
Polymers7,5524
Non-polymers1,5204
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.210, 32.210, 62.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Cell settingtetragonal
Space group name H-MP41

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Components

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


Mass: 1888.113 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PNI / TETRA[N-METHYL-PYRIDYL] PORPHYRIN-NICKEL


Mass: 735.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H36N8Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.25UM DNA, 1.25UM NI-PORPHYRIN, 50UM MGCL2, 5% MPD, 30MM SODIUM CACODYLATE, AGAINST 500UM RESERVOIR OF 55% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.25 mMDNA1drop
21.25 mMNi2+-TMPy1drop
350 mM1dropMgCl2
45 %MPD1drop
530 mMsodium cacodylate1drop
655 %MPD1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM1410.9189
SYNCHROTRONEMBL/DESY, HAMBURG X1120.9057
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
MARRESEARCH2IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91891
20.90571
ReflectionResolution: 0.86→30 Å / Num. obs: 45197 / % possible obs: 93 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.021
Reflection shellResolution: 0.9→1 Å / Redundancy: 8 % / Rmerge(I) obs: 0.124 / % possible all: 70.3
Reflection
*PLUS
Num. measured all: 336951

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Processing

Software
NameVersionClassification
CCP4MAD PROGSmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MAD PROGS)phasing
RefinementResolution: 0.9→6 Å / Num. parameters: 3867 / Num. restraintsaints: 0 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2
Stereochemistry target values: NO RESTRAINTS USED, THEREFORE THE RMSD DEVIATIONS ABOVE DO NOT HAVE ANY MEANING
Details: FULL-MATRIX LEAST-SQUARES
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2323 5 %RANDOM
Rwork0.152 ---
all0.151 42874 --
obs0.152 37075 --
Refinement stepCycle: LAST / Resolution: 0.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 772 196 202 1170
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 0.9 Å / Lowest resolution: 6 Å / σ(F): 4 / % reflection Rfree: 5 % / Rfactor obs: 0.142 / Rfactor Rfree: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS

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