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- PDB-4ez2: Crystal Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6... -

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Basic information

Entry
Database: PDB / ID: 4ez2
TitleCrystal Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 angstrom resolution
Components5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3'
KeywordsDNA / DNA four-way junction / Sodium ion
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChakraborty, A. / Mandal, P.K. / Gautham, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of d(CCGGGACCGG)(4) as a four-way junction at 1.6 A resolution: new insights into solvent interactions.
Authors: Chakraborty, A. / Mandal, P.K. / Gautham, N.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1653
Polymers6,1422
Non-polymers231
Water1,63991
1
A: 5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*GP*AP*CP*CP*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)12,3306
Polymers12,2844
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3020 Å2
ΔGint-20 kcal/mol
Surface area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.010, 24.350, 38.180
Angle α, β, γ (deg.)90.00, 112.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-101-

NA

21A-238-

HOH

31B-125-

HOH

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Components

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


Mass: 3071.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM sodium cacodylate trihydrate buffer (pH 7.0), 10mM MnCl2, 1mM spermine, 50% methyl pentane diol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 18, 2010 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→22.52 Å / Num. all: 7375 / Num. obs: 7323 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.45 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.6 / % possible all: 99

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 467D

467d


Resolution: 1.6→19.305 Å / SU ML: 0.17 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 341 4.68 %random
Rwork0.2163 ---
obs0.2179 7293 98.96 %-
all-7370 --
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.689 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2975 Å20 Å20.7075 Å2
2--2.9387 Å2-0 Å2
3----2.6412 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 1 91 500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005458
X-RAY DIFFRACTIONf_angle_d1.259704
X-RAY DIFFRACTIONf_dihedral_angle_d35.274192
X-RAY DIFFRACTIONf_chiral_restr0.06378
X-RAY DIFFRACTIONf_plane_restr0.00720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6-2.01550.29491740.25773422
2.0155-19.3060.23311670.20413530
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35780.1676-0.11790.1779-0.25810.43280.0272-0.0112-0.0084-0.0962-0.1133-0.11150.10390.1144-0.07860.11950.03280.02040.1358-0.00020.161-0.3361-0.242915.9588
20.21960.3188-0.22140.4888-0.40730.8414-0.3077-0.23640.01920.04610.2097-0.03160.170.0486-0.47130.09910.0583-0.02160.1977-0.01530.1134-4.26350.29248.5986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:10)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 11:20)

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