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- PDB-1o55: MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC AC... -

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Basic information

Entry
Database: PDB / ID: 1o55
TitleMOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION
ComponentsDNA (5'-CD(*AP*AP*AP)-3')
KeywordsDNA / CYCLIC TRINUCLEOTIDE
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.04 Å
AuthorsGao, Y.G. / Robinson, H. / Guan, Y. / Liaw, Y.C. / van Boom, J.H. / van der Marel, G.A. / Wang, A.H.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1998
Title: Molecular structure of two crystal forms of cyclic triadenylic acid at 1A resolution.
Authors: Gao, Y.G. / Robinson, H. / Guan, Y. / Liaw, Y.C. / van Boom, J.H. / van der Marel, G.A. / Wang, A.H.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionAug 26, 2003ID: 415d
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The crystallized entity is 5'-CD(*AP*AP*AP)-3', however, each of the two independent ...SEQUENCE The crystallized entity is 5'-CD(*AP*AP*AP)-3', however, each of the two independent molecules sits on the crystallographic 3-fold axis. Remark 350 provides the way to create cyclic D(*Ap*Ap*Ap) molecule.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-CD(*AP*AP*AP)-3')
B: DNA (5'-CD(*AP*AP*AP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8483
Polymers1,7892
Non-polymers591
Water41423
1
A: DNA (5'-CD(*AP*AP*AP)-3')

A: DNA (5'-CD(*AP*AP*AP)-3')

A: DNA (5'-CD(*AP*AP*AP)-3')


Theoretical massNumber of molelcules
Total (without water)2,6843
Polymers2,6843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
2
B: DNA (5'-CD(*AP*AP*AP)-3')
hetero molecules

B: DNA (5'-CD(*AP*AP*AP)-3')
hetero molecules

B: DNA (5'-CD(*AP*AP*AP)-3')
hetero molecules


  • defined by author
  • 2.86 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)2,8616
Polymers2,6843
Non-polymers1773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)22.637, 22.637, 44.581
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settinghexagonal
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-103-

HOH

21A-117-

HOH

31B-101-

HOH

41B-105-

HOH

51B-106-

HOH

61B-107-

HOH

71B-111-

HOH

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Components

#1: DNA chain DNA (5'-CD(*AP*AP*AP)-3')


Mass: 894.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic / Keywords: CYCLIC TRINUCLEOTIDE
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.67 Å3/Da / Density % sol: 26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1COCL311
2GLYCINE11
3MPD11
4MPD12

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 29, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.04→10 Å / Num. all: 2198 / Num. obs: 2198 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
bioteXdata collection
bioteXdata reduction
SHELXSphasing
SHELXL-97refinement
bioteXdata scaling
RefinementResolution: 1.04→10 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
all0.144 2198 -
obs0.138 2198 97.2 %
Refinement stepCycle: LAST / Resolution: 1.04→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 42 7 17 66
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.031
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

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