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- PDB-4gsg: DNA Holliday junction stabilized by chlorine halogen bond. Cl1J c... -

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Basic information

Entry
Database: PDB / ID: 4gsg
TitleDNA Holliday junction stabilized by chlorine halogen bond. Cl1J 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*(UCL)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 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 1.2Sep 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*AP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
C: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
D: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,2234
Polymers12,2234
Non-polymers00
Water2,864159
1
A: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
C: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
D: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')

A: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
C: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
D: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,4468
Polymers24,4468
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)65.578, 24.355, 37.243
Angle α, β, γ (deg.)90.000, 110.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-101-

HOH

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Components

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


Mass: 3029.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence
#2: DNA chain DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')


Mass: 3081.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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

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: Oct 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 6244 / Num. obs: 4947 / % possible obs: 79.2 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Biso Wilson estimate: 6.7 Å2

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Processing

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

2org


Resolution: 2→30.64 Å / Rfactor Rfree error: 0.022 / Occupancy max: 1 / Occupancy min: 0.15 / Data cutoff high absF: 35514 / 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
Rfree0.322 212 5.8 %RANDOM
Rwork0.271 ---
all-6244 --
obs-3667 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.8641 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 52.01 Å2 / Biso mean: 14.3574 Å2 / Biso min: 1.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å2-0.94 Å2
2--3.64 Å20 Å2
3----5.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 0 159 967
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.001
X-RAY DIFFRACTIONc_angle_deg0.4
X-RAY DIFFRACTIONc_dihedral_angle_d16.5
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.422.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 28 4.7 %
Rwork0.336 572 -
all-600 -
obs--95.4 %
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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