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- PDB-2wna: Crystal structure of the GNA 3'-G(Br)CGCGC-2' -

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Basic information

Entry
Database: PDB / ID: 2wna
TitleCrystal structure of the GNA 3'-G(Br)CGCGC-2'
ComponentsGNA
KeywordsRNA / GNA / NUCLEIC ACID / GLYCOL NUCLEIC ACID / WATSON-CRICK BASE PAIR
Function / homologyCOBALT HEXAMMINE(III) / RNA
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.97 Å
AuthorsSchlegel, M.K. / Essen, L.-O. / Meggers, E.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2010
Title: Atomic Resolution Duplex Structure of the Simplified Nucleic Acid Gna.
Authors: Schlegel, M.K. / Essen, L.-O. / Meggers, E.
#1: Journal: J.Am.Chem.Soc. / Year: 2008
Title: Duplex Structure of a Minimal Nucleic Acid.
Authors: Schlegel, M.K. / Essen, L.-O. / Meggers, E.
History
DepositionJul 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_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

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Assembly

Deposited unit
A: GNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9834
Polymers1,6371
Non-polymers3473
Water1,04558
1
A: GNA
hetero molecules

A: GNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9678
Polymers3,2742
Non-polymers6936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_855-x+3,y,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)20.420, 42.000, 28.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1001-

NCO

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Components

#1: RNA chain GNA


Mass: 1636.884 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SYNTHETIC GLYCOL NUCLEIC ACID, 3'-(S)-((ZGU)P(ZBC)P(ZGU)P(ZCY)P(ZGU)P(ZCY))-2'
Source: (synth.) HOMO SAPIENS (human)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#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.: 58 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details(S)-1'-(2',3'-DIHYDROXYPROPYL)-5-BROMO-CYTOSINE (ZBC): ZCY ANALOG BEARING A BROMINE AT C5 COBALT ...(S)-1'-(2',3'-DIHYDROXYPROPYL)-5-BROMO-CYTOSINE (ZBC): ZCY ANALOG BEARING A BROMINE AT C5 COBALT HEXAMMINE(III) (NCO): COBALT HEXAMINNE COMPLEXES SHOW DISORDER, CHARGE +3 MAGNESIUM ION (MG): CHARGE +2
Sequence detailsCYTOSINE A2 IS BROMINATED AT C5 FOR SAD ANALYSIS

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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: 1.41 Å3/Da / Density % sol: 12.73 %
Description: LOW AND HIGH RESOLUTION DATA MERGED FROM SAME CRYSTAL. DATA RECORDING OCCURED AT PEAK WAVELENGTH OF BROMINE
Crystal growpH: 5.5
Details: DROP: 2 MM G(BR)CGCGC, 10% 2-METHYL-2,4-PENTANEDIOL, 40 MM SODIUM CACODYLATE (PH 5.5), 20 MM COBALT HEXAMINE, 80 MM SODIUM CHLORIDE, 20 MM MAGNESIUM CHLORIDE RESERVOIR: 35 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91826
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91826 Å / Relative weight: 1
ReflectionResolution: 0.96→21 Å / Num. obs: 30224 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.99 % / Biso Wilson estimate: 4.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.7
Reflection shellResolution: 0.96→1.02 Å / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 7.2 / % possible all: 0.9

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Processing

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

Resolution: 0.97→8 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.434 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GNA DUPLEX OF TYPE N FORMED WITH SYMMETRY- EQUIVALENT MOLECULE
RfactorNum. reflection% reflectionSelection details
Rfree0.12726 533 7.1 %RANDOM
Rwork0.10503 ---
obs0.10648 7025 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.688 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 0.97→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 103 15 58 176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021150
X-RAY DIFFRACTIONr_bond_other_d00.0253
X-RAY DIFFRACTIONr_angle_refined_deg3.533220
X-RAY DIFFRACTIONr_angle_other_deg0.6983118
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_restr0.0480.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0264
X-RAY DIFFRACTIONr_gen_planes_other00.0223
X-RAY DIFFRACTIONr_nbd_refined0.0810.311
X-RAY DIFFRACTIONr_nbd_other0.2960.347
X-RAY DIFFRACTIONr_nbtor_refined0.2650.542
X-RAY DIFFRACTIONr_nbtor_other0.0760.530
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.450.546
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4490.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3210.558
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_it2.2242218
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7983203
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.2533405
X-RAY DIFFRACTIONr_sphericity_free10.469359
X-RAY DIFFRACTIONr_sphericity_bonded5.2293184
LS refinement shellResolution: 0.965→0.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.169 40 -
Rwork0.161 423 -
obs--83.88 %

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