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- PDB-1vro: Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoros... -

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Basic information

Entry
Database: PDB / ID: 1vro
TitleSelenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure
Components5'-D(*CP*(GMS)P*CP*GP*CP*G)-3'
KeywordsDNA / Left-handed Z-DNA / phosphoroselenoate / multiwavelength anomalous dispersion (MAD) / covalent modification of oligonucleotides / oligonucleotide analogue / phasing strategy / synchrotron
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.1 Å
AuthorsWilds, C.J. / Pattanayek, R. / Pan, C. / Wawrzak, Z. / Egli, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure
Authors: Wilds, C.J. / Pattanayek, R. / Pan, C. / Wawrzak, Z. / Egli, M.
History
DepositionApr 14, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionApr 19, 2005ID: 1n6s
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_asym_id / _struct_conn.ptnr2_label_atom_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

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*CP*(GMS)P*CP*GP*CP*G)-3'
B: 5'-D(*CP*(GMS)P*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9734
Polymers3,7462
Non-polymers2272
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.778, 31.348, 44.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 1873.166 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: synthesized with a solid-phase oligonucleotide synthesizer using DNA phosphoramidites and potassium selenocyanide for introducing the phosphoroselenoate linkage
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.32 Å3/Da / Density % sol: 5.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.5mM DNA, 4mM-15mM magnesium chloride, 50mM sodium cacodylate, 2mM-8mM spermine tetrahydrochloride and reservoir 30% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1DNA11
2MgCl11
3sodium cacodylate11
4spermine tetrahydrochloride11
5MPD12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9561, 0.9787, 0.9784
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 22, 2002
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95611
20.97871
30.97841
ReflectionResolution: 1.1→20 Å / Num. all: 10197 / Num. obs: 9718 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.47 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 22.7
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 7.47 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 15.85 / Num. unique all: 1802 / % possible all: 95.4

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.1→20 Å / Num. parameters: 3005 / Num. restraintsaints: 5144 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Shelx-97
RfactorNum. reflection% reflectionSelection details
Rfree0.129 508 -random
Rwork0.097 ---
all-9718 --
obs-9718 97.7 %-
Displacement parametersBiso mean: 6.9 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 245 15 73 333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.028
X-RAY DIFFRACTIONs_angle_d0.022

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