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- PDB-3s49: RNA crystal structure with 2-Se-uridine modification -

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Basic information

Entry
Database: PDB / ID: 3s49
TitleRNA crystal structure with 2-Se-uridine modification
ComponentsRNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
KeywordsRNA / 2-Se-uridine
Function / homology: / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSheng, J. / Gan, J. / Sun, H. / Hassan, A.E.H. / Jiang, S. / Huang, Z.
CitationJournal: To be Published
Title: Higher Specificity of RNA Base Pairing with 2-Selenouridine
Authors: Sheng, J. / Gan, J. / Sun, H. / Hassan, A.E.H. / Jiang, S. / Huang, Z.
History
DepositionMay 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_type.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

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
B: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
C: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
D: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
E: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
F: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
G: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,13910
Polymers18,0227
Non-polymers1173
Water1,27971
1
A: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
B: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1492
Polymers5,1492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
D: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1883
Polymers5,1492
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
F: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2274
Polymers5,1492
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')

G: RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1492
Polymers5,1492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Unit cell
Length a, b, c (Å)47.095, 47.095, 424.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-9-

K

21F-2-

K

31A-21-

HOH

41A-42-

HOH

51C-10-

HOH

61C-93-

HOH

71D-18-

HOH

81D-84-

HOH

91E-14-

HOH

101F-18-

HOH

111F-131-

HOH

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Components

#1: RNA chain
RNA (5'-R(*GP*UP*AP*UP*AP*(RUS)P*AP*C)-3')


Mass: 2574.506 Da / Num. of mol.: 7 / Source method: obtained synthetically / Details: 2-Se-U-phosphoramidite and solid phase synthesis
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% MPD, 40 mM Na Cacodylate (pH 7.0), 12mM Spermine Tetra-HCl, 80 mM Potassium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Aug 1, 2010
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 9870 / Num. obs: 8288 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.8 % / Rmerge(I) obs: 0.5109 / Net I/σ(I): 22
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 3.3 / Num. unique all: 959 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 246D

246d


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.327 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26977 421 4.9 %RANDOM
Rwork0.21484 ---
obs0.2173 8206 99.44 %-
all-8288 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.531 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å21.01 Å20 Å2
2--2.01 Å20 Å2
3----3.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.245 Å0.31 Å
Luzzati sigma a-0.174 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1162 3 71 1236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211295
X-RAY DIFFRACTIONr_angle_refined_deg1.16932002
X-RAY DIFFRACTIONr_chiral_restr0.0530.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02567
X-RAY DIFFRACTIONr_nbd_refined0.1420.2491
X-RAY DIFFRACTIONr_nbtor_refined0.2620.2824
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.219
X-RAY DIFFRACTIONr_scbond_it0.72931358
X-RAY DIFFRACTIONr_scangle_it1.0124.52002
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 29 -
Rwork0.306 606 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7303-1.27731.24624.7287-0.20390.60360.39180.1433-0.1266-0.30130.29020.2215-0.0771-0.8166-0.682-0.0923-0.0135-0.01440.03330.0993-0.02713.273314.04257.937
26.18683.25194.65712.90842.979312.44880.4692-0.4684-0.39010.14240.17760.45910.4488-0.9091-0.6468-0.21360.0201-0.0559-0.13230.1753-0.017512.688710.30812.0779
32.46681.1165-0.17161.0167-0.33093.11350.4957-0.20340.43430.4124-0.16360.2315-0.52350.2837-0.3321-0.0195-0.03380.0987-0.1101-0.0314-0.05661.088312.491932.3518
42.8828-0.8505-1.4132.60321.0460.86080.18760.24630.32910.09980.23510.00610.01510.0751-0.4227-0.0188-0.03670.0559-0.05830.0296-0.04282.7829.364728.2688
50.6154-0.8598-0.65772.81282.07697.61970.0337-0.2032-0.17710.55330.3929-0.3010.58110.3231-0.4266-0.02280.0792-0.1177-0.0618-0.0512-0.10258.520217.883853.0478
64.7465-1.6609-0.15012.19770.93136.6472-0.0886-0.0768-0.28790.29890.4707-0.41160.4584-0.0613-0.3821-0.07260.0101-0.0825-0.1418-0.0711-0.10835.081118.875249.012
710.23212.32485.86364.60633.923416.46231.33940.0766-1.27970.4680.4988-0.16372.69770.4792-1.83810.71770.3474-0.29860.0064-0.05830.02538.47969.863273.2859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION2B9 - 16
3X-RAY DIFFRACTION3C1 - 8
4X-RAY DIFFRACTION4D9 - 16
5X-RAY DIFFRACTION5E1 - 8
6X-RAY DIFFRACTION6F9 - 16
7X-RAY DIFFRACTION7G1 - 8

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