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- PDB-363d: High-resolution crystal structure of a fully modified N3'-> P5' p... -

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Entry
Database: PDB / ID: 363d
TitleHigh-resolution crystal structure of a fully modified N3'-> P5' phosphoramidate DNA dodecamer duplex
Components5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
KeywordsDNA / A-DNA / MODIFIED
Function / homologyAMMONIUM ION / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTereshko, V. / Gryaznov, S. / Egli, M.
CitationJournal: J.Am.Chem.Soc. / Year: 1998
Title: Consequences of Replacing the DNA 3'-Oxygen by an Amino Group: High-Resolution Crystal Structure of a Fully Modified N3'--> P5' Phosphoramidate DNA Dodecamer Duplex
Authors: Tereshko, V. / Gryaznov, S. / Egli, M.
History
DepositionNov 26, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 15, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
B: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
C: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
D: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
E: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
F: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,77442
Polymers21,9156
Non-polymers85836
Water3,603200
1
A: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
B: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,59114
Polymers7,3052
Non-polymers28612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
D: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,59114
Polymers7,3052
Non-polymers28612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
F: 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,59114
Polymers7,3052
Non-polymers28612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.150, 40.150, 304.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-237-

NH4

21A-239-

NH4

31A-255-

CL

41A-226-

NH4

51A-228-

NH4

61A-250-

CL

71B-238-

NH4

81B-240-

NH4

91B-256-

CL

101B-225-

NH4

111B-227-

NH4

121B-249-

CL

131C-243-

NH4

141C-245-

NH4

151C-259-

CL

161C-244-

NH4

171C-248-

NH4

181C-260-

CL

191D-242-

NH4

201D-246-

NH4

211D-258-

CL

221D-241-

NH4

231D-247-

NH4

241D-257-

CL

251E-229-

NH4

261E-235-

NH4

271E-251-

CL

281E-230-

NH4

291E-234-

NH4

301E-252-

CL

311F-232-

NH4

321F-231-

NH4

331F-236-

NH4

341F-254-

CL

351F-233-

NH4

361F-253-

CL

371E-381-

HOH

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Components

#1: DNA chain
5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM)P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'


Mass: 3652.559 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
#2: Chemical...
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: H4N
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NH4CL11
3MGCL211
4NA HEPES11
51,6-HEXANEDIOL11
6WATER12
7NH4CL12
8MGCL212
9NA HEPES12
101,6-HEXANEDIOL12
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / PH range low: 7.4 / PH range high: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.5 mMphosphoramidate dodecamer1drop
240 mMsodium cacodylate1drop
310-500 mM1dropcan be replaced by CaCl2MgCl2
41-30 mMspermine tetrahydrochloride1drop
520-40 %MPD1reservoir
61
71
81
91
101

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→34 Å / Num. obs: 6737 / % possible obs: 98.4 % / Rmerge(I) obs: 0.082
Reflection shellHighest resolution: 2 Å / Redundancy: 11.4 %
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 34 Å / % possible obs: 98.4 % / Num. measured all: 76542

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A-FORM DUPLEX

Resolution: 2→8 Å / Cross valid method: FREE R-VALUE / σ(F): 2
Details: THE CRYSTAL IS A PRECISE MEROHEDRAL TWIN AND THE COORDINATES REPRESENT ONE COLUMN CONSISTING OF THREE DODECAMER DUPLEXES (ALL ATOMS WITH OCCUPANCY 0.5, HALF THE WATERS HAVE OCCUPANCY 1.0, ...Details: THE CRYSTAL IS A PRECISE MEROHEDRAL TWIN AND THE COORDINATES REPRESENT ONE COLUMN CONSISTING OF THREE DODECAMER DUPLEXES (ALL ATOMS WITH OCCUPANCY 0.5, HALF THE WATERS HAVE OCCUPANCY 1.0, THE OTHER HALF ZERO). TOTAL NUMBER OF SOLVENT ATOMS REFERS TO R3 ASYMMETRIC UNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -15 %RANDOM
Rwork0.192 ---
all0.2 ---
obs0.192 5854 86.9 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1524 36 200 1760
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 15 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_improper_angle_deg1.59

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