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- PDB-2jja: Crystal structure of GNA with synthetic copper base pair -

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Entry
Database: PDB / ID: 2jja
TitleCrystal structure of GNA with synthetic copper base pair
ComponentsGNA
KeywordsRNA / NUCLEIC ACID / SYNTHETIC BASE PAIR / GLYCOL NUCLEIC ACID / GNA
Function / homologyCOPPER (II) ION / COBALT HEXAMMINE(III) / RNA
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsSchlegel, M.K. / Essen, L.-O. / Meggers, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Duplex Structure of a Minimal Nucleic Acid.
Authors: Schlegel, M.K. / Essen, L.-O. / Meggers, E.
History
DepositionMar 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: 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 / Other / Polymer sequence
Category: chem_comp / database_2 ...chem_comp / database_2 / entity_poly / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Revision 2.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5377
Polymers2,0791
Non-polymers4576
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)18.160, 48.590, 59.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1004-

NCO

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain GNA


Mass: 2079.336 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 3'-(S)-((ZCY)P(ZGU)P(ZHP)P(ZAD)P(ZTH)P(ZHP)P(ZCY)P (ZGU))-2'
Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 86 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details(S)-1-(2,3-DIHYDROXYPROPYL)-HYDROXYPYRIDONE (ZHP): COPPER-CHELATING ARTIFICIAL BASE

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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: 2.02 Å3/Da / Density % sol: 38.5 % / Description: NONE
Crystal growpH: 5.5
Details: 10% MPD, 40 MM SODIUM CACODYLATE, PH=5.5, 20 MM COBALT HEXAMINE, 80 MM NACL, 20 MM MGCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 24, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.3→10 Å / Num. obs: 7095 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.4
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.3→10 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.3 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.148 479 7.1 %RANDOM
Rwork0.124 ---
obs0.126 6289 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2--0.91 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 136 18 80 234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02160
X-RAY DIFFRACTIONr_bond_other_d0.0070.0276
X-RAY DIFFRACTIONr_angle_refined_deg2.0743219
X-RAY DIFFRACTIONr_angle_other_deg0.9553163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0232
X-RAY DIFFRACTIONr_nbd_refined0.0920.216
X-RAY DIFFRACTIONr_nbd_other0.1880.2102
X-RAY DIFFRACTIONr_nbtor_refined0.2730.254
X-RAY DIFFRACTIONr_nbtor_other0.0850.242
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5450.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1622195
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7553219
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.226 33
Rwork0.191 432

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