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- PDB-2gjb: Crosslinking of DNA duplexes: X-ray crystal structure of an unsub... -

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Basic information

Entry
Database: PDB / ID: 2gjb
TitleCrosslinking of DNA duplexes: X-ray crystal structure of an unsubstituted bisacridine with the oligonucleotide d(CGTACG)
Components5'-D(*CP*GP*TP*AP*CP*GP*)-3'
KeywordsDNA / DNA duplex / bis-intercalator
Function / homologyChem-BMO / : / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGan, Y. / Cardin, C.J. / Denny, W.A.
CitationJournal: To be Published
Title: Crosslinking of DNA duplexes: X-ray crystal structure of an unsubstituted bisacridine with oligonucleotide d(CGTACG)
Authors: Gan, Y. / Cardin, C.J. / Denny, W.A.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 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(*CP*GP*TP*AP*CP*GP*)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3343
Polymers1,8091
Non-polymers5252
Water181
1
A: 5'-D(*CP*GP*TP*AP*CP*GP*)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,6686
Polymers3,6182
Non-polymers1,0494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Unit cell
Length a, b, c (Å)25.750, 25.750, 78.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-8-

BMO

DetailsThe second part of the biological assembly is generated by the two fold axis

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-BMO / N-ACRIDIN-9-YL-N'-[3-(ACRIDIN-9-YLAMINO)PROPYL]PROPANE-1,3-DIAMINE / 1,3-PROPANEDIAMINE / N-9-ACRIDINYL-N -[3-(9-ACRIDINYLAMINO)PROPYL]


Mass: 485.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H31N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 38.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The crystals grow in ten days from sitting drops containing 2mM DNA, 12mM spermine, 80mM strontium chloride, 20mM magnesium chloride, 10%MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1spermine11
2strontium chloride11
3magnesium chloride11
4MPD11
5H2O11
6strontium chloride12
7magnesium chloride12
8MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→22.3 Å / Num. obs: 1472 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 20.1 % / Biso Wilson estimate: 57.431 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 49.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 9 / Num. unique all: 204 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY DD0018

Resolution: 2.2→8 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.648 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30508 45 4.8 %RANDOM
Rwork0.27002 ---
all0.358 ---
obs0.27223 890 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.613 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å21.05 Å20 Å2
2--2.09 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 20 1 141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021155
X-RAY DIFFRACTIONr_angle_refined_deg3.3912.996233
X-RAY DIFFRACTIONr_chiral_restr0.1650.223
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0277
X-RAY DIFFRACTIONr_nbd_refined0.2740.227
X-RAY DIFFRACTIONr_nbtor_refined0.3710.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.25
X-RAY DIFFRACTIONr_scbond_it3.4833173
X-RAY DIFFRACTIONr_scangle_it5.2244.5233
LS refinement shellResolution: 2.2→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.583 4 -
Rwork0.367 58 -
obs--100 %

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