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- PDB-1z7i: 2'-Me-Se Derivitation of A-DNA Octamer G(UMSe)GTACAC -

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Basic information

Entry
Database: PDB / ID: 1z7i
Title2'-Me-Se Derivitation of A-DNA Octamer G(UMSe)GTACAC
Components5'-D(*GP*(UMS)P*GP*TP*AP*CP*AP*C)-3'
KeywordsDNA / 2'-Methylseleno-uridine / Se-DNA / Selenium Derivatization
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsHuang, Z. / Carrasco, N. / Jiang, J.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Selenium derivatization of nucleic acids for crystallography.
Authors: Jiang, J. / Sheng, J. / Carrasco, N. / Huang, Z.
History
DepositionMar 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 14, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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 / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,7082
Polymers2,5061
Non-polymers2021
Water79344
1
A: 5'-D(*GP*(UMS)P*GP*TP*AP*CP*AP*C)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,4164
Polymers5,0112
Non-polymers4052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.076, 42.076, 23.935
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-82-

HOH

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Components

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


Mass: 2505.577 Da / Num. of mol.: 1 / Fragment: 2'-Selenium A-DNA DUPLEX / Source method: obtained synthetically
Details: Solid Phase Synthesis via Phosphoramidite Chemistry
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.01 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% v/v MPD, 40 mM Sodium Cacodylate (pH 6.0), 12 mM Spermine tetra-HCl, 80 mM Sodium Chloride, 20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Sodium Cacodylate11
3Spermine tetra-HCl11
4Sodium Chloride11
5Magnesium Chloride11
6H2O11
7MPD12
8Sodium Cacodylate12
9Sodium Chloride12
10Magnesium Chloride12

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979, 0.9794, 0.940, 0.920
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 13, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97941
30.941
40.921
ReflectionResolution: 1.28→50 Å / Num. all: 6325 / Num. obs: 6029 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 1.28→1.3 Å / % possible all: 70

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.28→20.81 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 450767.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: dna-rna_ums.par
RfactorNum. reflection% reflectionSelection details
Rfree0.2 581 11 %RANDOM
Rwork0.177 ---
all0.182 5901 --
obs0.177 5275 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.2222 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.28→20.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 162 3 44 209
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d33.1
X-RAY DIFFRACTIONc_improper_angle_d2.07
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.52
X-RAY DIFFRACTIONc_scbond_it1.282
X-RAY DIFFRACTIONc_scangle_it1.922.5
LS refinement shellResolution: 1.28→1.36 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 81 12.8 %
Rwork0.237 552 -
obs--66.6 %
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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