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- PDB-4gsi: DNA Holliday junction stabilized by fluorine halogen bond. F2J co... -

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Basic information

Entry
Database: PDB / ID: 4gsi
TitleDNA Holliday junction stabilized by fluorine halogen bond. F2J construct of related reference.
Components
  • DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
  • DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UFP)P*CP*GP*G)-3')
KeywordsDNA / DNA Holliday junction / halogen bond
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHo, P.S. / Carter, M.
CitationJournal: Biochemistry / Year: 2013
Title: Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.
Authors: Carter, M. / Voth, A.R. / Scholfield, M.R. / Rummel, B. / Sowers, L.C. / Ho, P.S.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_comp_id / _struct_conn.ptnr2_label_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*GP*TP*AP*(UFP)P*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
C: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UFP)P*CP*GP*G)-3')
D: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
E: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
F: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UFP)P*CP*GP*G)-3')
G: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
H: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UFP)P*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,3808
Polymers24,3808
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.213, 23.917, 77.450
Angle α, β, γ (deg.)90.000, 114.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-311-

HOH

21H-302-

HOH

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Components

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


Mass: 3064.968 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence
#2: DNA chain
DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')


Mass: 3029.994 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.27 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 0.7mM DNA, 25mM sodium cacodylate pH 7.0 buffer, 10-25mM calcium chloride, and 0.8-1.2mM spermine, equilibrated against a reservoir of 30-40% aqueous MPD, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.04→55 Å / Num. all: 6763 / Num. obs: 3910 / % possible obs: 24.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.066 / Χ2: 5.397 / Net I/σ(I): 23
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.04-2.133.40.207263.31413.3
2.13-2.244.50.2821724.319122.3
2.24-2.3850.2653951.649149.9
2.38-2.565.20.2455564.698171.1
2.56-2.825.60.2026026.298175.7
2.82-3.235.60.0996284.485178
3.23-4.075.20.0686919.417185.8
4.07-556.20.0458404.656199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ORG

2org


Resolution: 2.38→32.61 Å / Rfactor Rfree error: 0.022 / Occupancy max: 1 / Occupancy min: 0.4 / Data cutoff high absF: 27432 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.291 180 5.3 %RANDOM
Rwork0.225 ---
all-4947 --
obs-3398 74.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.8826 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 39.21 Å2 / Biso mean: 15.9929 Å2 / Biso min: 0.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å20.88 Å2
2--3.58 Å20 Å2
3----6.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.38→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1616 0 100 1716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.002
X-RAY DIFFRACTIONc_angle_deg0.6
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.38→2.53 Å / Rfactor Rfree error: 0.065 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 31 8.2 %
Rwork0.331 347 -
all-378 -
obs--51.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1mcdna-rna_rep.parammcdna-rna.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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