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- PDB-1fhy: PSORALEN CROSS-LINKED D(CCGCTAGCGG) FORMS HOLLIDAY JUNCTION -

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Basic information

Entry
Database: PDB / ID: 1fhy
TitlePSORALEN CROSS-LINKED D(CCGCTAGCGG) FORMS HOLLIDAY JUNCTION
ComponentsDNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')
KeywordsDNA / psoralen / cross-linked DNA / Holliday junction / 4-way junction / DNA-drug complex
Function / homology4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEichman, B.F. / Mooers, B.H.M. / Alberti, M. / Hearst, J.E. / Ho, P.S.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions.
Authors: Eichman, B.F. / Mooers, B.H. / Alberti, M. / Hearst, J.E. / Ho, P.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions
Authors: Eichman, B.F. / Vargason, J.M. / Mooers, B.H.M. / Ho, P.S.
History
DepositionAug 2, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 21, 2001Provider: 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.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.ptnr1_symmetry / _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.ptnr2_symmetry / _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(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3904
Polymers6,0922
Non-polymers2982
Water46826
1
A: DNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)12,7818
Polymers12,1844
Non-polymers5974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)70.674, 23.769, 44.339
Angle α, β, γ (deg.)90.00, 130.11, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsA four-way junction is a dimer constructed from chains A and B and a symmetry partner generated by the two-fold

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Components

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


Mass: 3045.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA IS CROSS-LINKED BY PSORALEN
#2: Chemical ChemComp-PSO / 4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN


Mass: 258.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium cacodylate, MgCl2, MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2MgCl211
3MPD11
4MgCl212
5MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mM1drop
2150 mM1dropMgCl2
30.5 mMspermine-HCl1drop
410 %(v/v)MPD1drop
520 %(v/v)1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→34.65 Å / Num. all: 10418 / Num. obs: 2937 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Num. unique all: 299 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 10418
Reflection shell
*PLUS
% possible obs: 99.3 % / Mean I/σ(I) obs: 8.2

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Processing

Software
NameVersionClassification
EPMRphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.65 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Parkinson et al.
Details: ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 316 10.8 %random
Rwork0.245 ---
all0.248 2928 --
obs0.248 2928 97.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.1053 Å20 Å2-8.523 Å2
2--28.494 Å20 Å2
3----12.3887 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 20 26 450
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.574
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 34.7 Å / Rfactor Rfree: 0.283
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.717

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