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- PDB-2x2q: Crystal structure of an 'all locked' LNA duplex at 1.9 angstrom r... -

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Basic information

Entry
Database: PDB / ID: 2x2q
TitleCrystal structure of an 'all locked' LNA duplex at 1.9 angstrom resolution
Components(LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM ...) x 2
KeywordsDNA / MODIFIED NUCLEIC ACID / LOCKED NUCLEIC ACID / THERMOSTABILITY
Function / homologyCACODYLATE ION / COBALT HEXAMMINE(III) / RNA
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEichert, A. / Behling, K. / Fuerste, J.P. / Betzel, C. / Erdmann, V.A. / Foerster, C.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: The Crystal Structure of an 'All Locked' Nucleic Acid Duplex.
Authors: Eichert, A. / Behling, K. / Betzel, C. / Erdmann, V.A. / Furste, J.P. / Forster, C.
History
DepositionJan 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn ...pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.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_conn.ptnr2_symmetry
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
B: LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
C: LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
D: LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7217
Polymers9,3984
Non-polymers3223
Water1,802100
1
A: LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
B: LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8603
Polymers4,6992
Non-polymers1611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
D: LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8604
Polymers4,6992
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.913, 40.737, 30.059
Angle α, β, γ (deg.)90.00, 91.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 7
2111C1 - 7
1121B8 - 14
2121D8 - 14

NCS ensembles :
ID
1
2

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Components

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LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM ... , 2 types, 4 molecules ACBD

#1: RNA chain LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX


Mass: 2284.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: RNA chain LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX


Mass: 2414.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 103 molecules

#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.48 Å3/Da / Density % sol: 66.5 % / Description: NONE
Crystal growpH: 5.5
Details: 40 MM SODIUM CACODYLATE (PH 5.5), 20 MM COBALT HEXAMMINE, 80 MM SODIUM CHLORIDE, 20 MM MAGNESIUM CHLORIDE, 10% (V/V) MPD EQILIBRATED AGAINST 35% (V/V) MPD (PH 7.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: May 8, 2009 / Details: MIRRORS, COLLIMATING AND FOCUSING, PT-COATED
RadiationMonochromator: DOUBLE CRYSTAL SI111 OR WHITE BEAM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38.95 Å / Num. obs: 7382 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GVN

3gvn


Resolution: 1.9→38.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.599 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 352 4.8 %RANDOM
Rwork0.22353 ---
obs0.22551 7030 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.235 Å2
Baniso -1Baniso -2Baniso -3
1--3.13 Å20 Å20.11 Å2
2---0.73 Å20 Å2
3---3.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 628 13 100 741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.3713.5521199
X-RAY DIFFRACTIONr_angle_other_deg
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_restr0.1220.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
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_it1.8613732
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3314.51199
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A152tight positional0.090.05
12C152tight positional0.090.05
21B162tight positional0.090.05
22D162tight positional0.090.05
11A152tight thermal0.410.5
12C152tight thermal0.410.5
21B162tight thermal0.420.5
22D162tight thermal0.420.5
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 29 -
Rwork0.328 507 -
obs--96.93 %

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