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- PDB-2gb9: d(CGTACG)2 crosslinked bis-acridine complex -

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Basic information

Entry
Database: PDB / ID: 2gb9
Titled(CGTACG)2 crosslinked bis-acridine complex
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / DNA DUPLEX CROSSLINKING
Function / homologyChem-A4C / STRONTIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsHopcroft, N.H. / Brogden, A.L. / Searcey, M. / Cardin, C.J.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative.
Authors: Hopcroft, N.H. / Brogden, A.L. / Searcey, M. / Cardin, C.J.
History
DepositionMar 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: 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.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN A4C 301 AND A4C 302 REPRESENT TWO CRYSTALLOGRAPHICALLY DISTINCT COPIES OF THE LIGAND. ...HETEROGEN A4C 301 AND A4C 302 REPRESENT TWO CRYSTALLOGRAPHICALLY DISTINCT COPIES OF THE LIGAND. EACH OF THESE TWO MOLECULES LIES ON A CRYSTALLOGRAPHIC AXIS OF TWO-FOLD ROTATIONAL SYMMETRY. HENCE, IN BOTH CASES, ONLY HALF OF THE LIGAND IS PRESENT IN THE COORDINATE FILE SUBMITTED, WHICH CORRESPONDS TO ONE ASYMMETRIC UNIT. THE OTHER HALF OF EACH LIGAND CAN BE GENERATED THROUGH SYMMETRY. LINKS ARE PROVIDED BETWEEN SYMMETRY RELATED CX3 ATOMS.

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


Theoretical massNumber of molelcules
Total (without water)5,1916
Polymers3,6182
Non-polymers1,5734
Water1,856103
1
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)15,57418
Polymers10,8556
Non-polymers4,71912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Unit cell
Length a, b, c (Å)37.210, 37.210, 53.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-202-

SR

21A-207-

HOH

31B-334-

HOH

41B-345-

HOH

51B-357-

HOH

DetailsThe other halves of the two drugs in the asymmetric unit are generated by the symmetry operations (1-x,y,-z) and (x,1-y,-z+0.5) respectively.

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Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-A4C / 9,9'-(HEXANE-1,6-DIYLDIIMINO)BIS{N-[2-(DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE}


Mass: 698.899 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H50N8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: SODIUM CACODYLATE pH7.0, SrCl2, SPERMINE, MPD, SITTING DROP VAPOUR DIFFUSION AT 291K, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2SrCl211
3SPERMINE11
4MPD11
5H2O11
6SODIUM CACODYLATE12
7SrCl212
8MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.769 / Wavelength: 0.769 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.769 Å / Relative weight: 1
ReflectionResolution: 1.7→37.2 Å / Num. all: 4509 / Num. obs: 4509 / % possible obs: 100 % / Redundancy: 26.8 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 4.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 27.9 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.4 / Num. unique all: 626 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
HKL2Mapmodel building
SHELXL-97refinement
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→8 Å / Num. parameters: 1589 / Num. restraintsaints: 1895 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 221 5 %RANDOM
Rwork0.213 ---
all-4204 --
obs-4204 95 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 393
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 54 103 397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0045
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.063
X-RAY DIFFRACTIONs_approx_iso_adps0

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