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- PDB-2dlj: 2'-Me-Se and Br Derivitation of A-DNA Octamer G(UMS)G(BRU)ACAC -

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Basic information

Entry
Database: PDB / ID: 2dlj
Title2'-Me-Se and Br Derivitation of A-DNA Octamer G(UMS)G(BRU)ACAC
Components5'-D(*GP*(UMS)P*GP*(BRU)P*AP*CP*AP*C)-3'
KeywordsDNA / 2'-Methylseleno-uridine / Se-DNA / Se-Br-DNA / Selenium Derivatization
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsJiang, J. / Huang, Z.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Selenium derivatization of nucleic acids for crystallography.
Authors: Jiang, J. / Sheng, J. / Carrasco, N. / Huang, Z.
History
DepositionApr 19, 2006Deposition site: PDBJ / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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*(BRU)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)2,5701
Polymers2,5701
Non-polymers00
Water81145
1
A: 5'-D(*GP*(UMS)P*GP*(BRU)P*AP*CP*AP*C)-3'

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


Theoretical massNumber of molelcules
Total (without water)5,1412
Polymers5,1412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.369, 42.369, 23.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 2570.447 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Solid Phase Synthesis via Phosphoramidite Chemistry
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 38.44 %
Crystal growTemperature: 298 K / pH: 6
Details: 10% v/v MPD 40mM Sodium Cacodylate, 12mM Spermine tetra-HCI, 80 mM sodium Chloride/12mM Potassium Chloride, 20 mM Magnesium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.00

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1, 0.9196
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2SINGLE WAVELENGTHMx-ray1
1SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.91961
ReflectionResolution: 1.5→18.61 Å / Num. obs: 3777 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 7.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.5 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
CBASSdata collection
HKL-2000data scaling
SOLVEphasing
RefinementResolution: 1.5→18.61 Å / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22 359 9.6 %RANDOM
Rwork0.174 ---
obs0.174 3597 95.8 %-
all-3597 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.92 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 18.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.272 Å20 Å20 Å2
2--0.272 Å20 Å2
3----0.543 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.5→18.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 162 0 45 207
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1921.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.5232
X-RAY DIFFRACTIONc_scangle_it2.0752.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.225 59 -
Rwork0.192 --
obs--11.1 %
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

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