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- PDB-2nsk: Doubled Modified Selenium DNA -

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Basic information

Entry
Database: PDB / ID: 2nsk
TitleDoubled Modified Selenium DNA
Components5'-D(*GP*(UMS)P*GP*(T4S)P*AP*CP*AP*C)-3'
KeywordsDNA / Double Modified Se-DNA / MAD/SAD Phasing
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJiang, J. / Shen, J. / Huang, Z.
CitationJournal: To be Published
Title: Double Modified Selinium DNA [G(Use)G(Tse)ACAC]
Authors: Jiang, J. / Shen, J. / Huang, Z.
History
DepositionNov 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*(UMS)P*GP*(T4S)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)2,5691
Polymers2,5691
Non-polymers00
Water64936
1
A: 5'-D(*GP*(UMS)P*GP*(T4S)P*AP*CP*AP*C)-3'

A: 5'-D(*GP*(UMS)P*GP*(T4S)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1372
Polymers5,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)42.305, 42.305, 23.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-40-

HOH

DetailsDuplex can be generated by (y,x,-z)

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Components

#1: DNA chain 5'-D(*GP*(UMS)P*GP*(T4S)P*AP*CP*AP*C)-3'


Mass: 2568.538 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% MPD, 40mM NaCacodylate pH 7.0 , 12 mMSpermine tetra-HCI, and 80 mM Soldium Chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2NaCacodylate11
3Spermine tetra-HCI11
4Soldium Chloride11
5H2O11
6MPD12
7NaCacodylate12
8Soldium Chloride12
9H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1000, 0.9796, 0.9798, 0.9400
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 7, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97961
30.97981
40.941
ReflectionResolution: 1.5→40 Å / Num. all: 3718 / Num. obs: 3718 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 5.6 / Num. unique all: 352 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→15.82 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 616408.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5
RfactorNum. reflection% reflectionSelection details
Rfree0.212 273 7.7 %RANDOM
Rwork0.195 ---
all0.198 3531 --
obs0.195 3531 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.6183 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2---1.51 Å20 Å2
3---3.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→15.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 162 0 36 198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d32.2
X-RAY DIFFRACTIONc_improper_angle_d2.17
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.199 35 6.6 %
Rwork0.195 492 -
obs-492 88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4dna-rna_ums.parion.top
X-RAY DIFFRACTION5cac.parums.top

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