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- PDB-1dpl: A-DNA DECAMER GCGTA(T23)TACGC WITH INCORPORATED 2'-METHOXY-3'-MET... -

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Basic information

Entry
Database: PDB / ID: 1dpl
TitleA-DNA DECAMER GCGTA(T23)TACGC WITH INCORPORATED 2'-METHOXY-3'-METHYLENEPHOSPHATE-THYMIDINE
Components5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'
KeywordsDNA / MODIFIED A-DECAMER AT 0.83 A RESOLUTION / DEOXYRIBONUCLEIC ACID
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.83 Å
AuthorsEgli, M. / Tereshko, V. / Teplova, M. / Minasov, G. / Joachimiak, A. / Sanishvili, R. / Weeks, C.M. / Miller, R. / Maier, M.A. / An, H. ...Egli, M. / Tereshko, V. / Teplova, M. / Minasov, G. / Joachimiak, A. / Sanishvili, R. / Weeks, C.M. / Miller, R. / Maier, M.A. / An, H. / Dan Cook, P. / Manoharan, M.
CitationJournal: Biopolymers / Year: 1998
Title: X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution.
Authors: Egli, M. / Tereshko, V. / Teplova, M. / Minasov, G. / Joachimiak, A. / Sanishvili, R. / Weeks, C.M. / Miller, R. / Maier, M.A. / An, H. / Dan Cook, P. / Manoharan, M.
History
DepositionDec 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 22, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / database_2 ...chem_comp / database_2 / entity_poly / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct_conn / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 2.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5996
Polymers6,1462
Non-polymers4534
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.627, 42.717, 46.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'


Mass: 3073.059 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: SPERMINE, MGCL2, NACL, KCL, SODIUM CACODYLATE BUFFER, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1SPERMINE11
2SODIUM CACODYLATE BUFFER11
3MGCL211
4NACLSodium chloride11
5KCL11
6MGCL212
7NACLSodium chloride12
8KCL12
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.25 mMdecamer1dropsingle strand
220 mMsodium cacodylate1drop
36 mMspermine1drop
410 mM1dropMg2+
540 mM1dropK+
635 %(v/v)MPD1reservoir
71
81

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.83→20 Å / Num. all: 47403 / Num. obs: 47403 / % possible obs: 99.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 0.83→0.9 Å / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 422954

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
SHELXL-97refinement
RefinementResolution: 0.83→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.121 4742 10 %RANDOM
Rwork0.115 ---
all0.117 47403 --
obs0.117 47403 99.7 %-
Refinement stepCycle: LAST / Resolution: 0.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 447 26 177 650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.037
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 0.83 Å / Lowest resolution: 0.9 Å / Num. reflection obs: 9963 / Rfactor obs: 0.129

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