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- PDB-4nfo: Crystal Structure Analysis of the 16mer GCAGACUUAAGUCUGC -

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Basic information

Entry
Database: PDB / ID: 4nfo
TitleCrystal Structure Analysis of the 16mer GCAGACUUAAGUCUGC
ComponentsGCAGACUUAAGUCUGC
KeywordsRNA / RNA 16mer oligo
Function / homologySPERMINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBeal, P.A. / Fisher, A.J. / Phelps, K.J. / Ibarra-Soza, J.M. / Zheng, Y.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA.
Authors: Phelps, K.J. / Ibarra-Soza, J.M. / Tran, K. / Fisher, A.J. / Beal, P.A.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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

Downloads & links

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Assembly

Deposited unit
A: GCAGACUUAAGUCUGC
B: GCAGACUUAAGUCUGC
C: GCAGACUUAAGUCUGC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4974
Polymers15,2943
Non-polymers2021
Water39622
1
A: GCAGACUUAAGUCUGC

A: GCAGACUUAAGUCUGC


Theoretical massNumber of molelcules
Total (without water)10,1962
Polymers10,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area1510 Å2
ΔGint-8 kcal/mol
Surface area5870 Å2
MethodPISA
2
B: GCAGACUUAAGUCUGC
C: GCAGACUUAAGUCUGC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3983
Polymers10,1962
Non-polymers2021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-9 kcal/mol
Surface area5980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.980, 43.080, 48.760
Angle α, β, γ (deg.)90.00, 120.98, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: C / End label comp-ID: C / Refine code: 0 / Auth seq-ID: 1 - 16 / Label seq-ID: 1 - 16

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3
DetailsAsymmetric unit contains 1.5 RNA duplexes

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Components

#1: RNA chain GCAGACUUAAGUCUGC


Mass: 5098.079 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% MPD(v/v)(Drop), 35% MPD(v/v)(reservoir), 40mM Na-cacodylate trihydrate (pH 7), 12mM spermine tetrahydrochloride, 80mM SrCl2, 20mM MgCl2 hexahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.148 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2012
RadiationMonochromator: Si(111) Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.148 Å / Relative weight: 1
ReflectionResolution: 1.96→35.81 Å / Num. all: 9759 / Num. obs: 9115 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 17.06
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.19 / Num. unique all: 706 / % possible all: 96.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→35.81 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.972 / SU B: 13.127 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.214 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 443 4.9 %RANDOM
Rwork0.21709 ---
all0.21839 9115 --
obs0.21839 8672 93.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.364 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å2-0.93 Å2
2--1.81 Å20 Å2
3----1.92 Å2
Refine analyzeLuzzati coordinate error free: 0.171 Å
Refinement stepCycle: LAST / Resolution: 1.96→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1011 14 22 1047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0111141
X-RAY DIFFRACTIONr_bond_other_d0.0090.02497
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.2911764
X-RAY DIFFRACTIONr_angle_other_deg1.71431203
X-RAY DIFFRACTIONr_chiral_restr0.0820.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02568
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02252
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A919
12B919
21A919
22C919
31B923
32C923
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 27 -
Rwork0.379 651 -
obs-651 97.13 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.42432.8779-1.310813.6947-1.12388.59520.36610.61660.2664-0.1220.10650.53420.367-0.1017-0.47260.08380.0208-0.01260.19380.08640.093558.686521.57134.9369
25.8119-1.6194-2.03876.20444.38273.24630.6580.72170.287-0.3007-0.4622-0.0774-0.3226-0.3688-0.19580.19810.02550.00650.14380.04660.10669.0120.494424.1121
34.26171.36693.57321.10550.05374.78730.28940.5431-0.51840.170.1552-0.15620.10870.4677-0.44460.13550.0512-0.12880.1466-0.07390.148759.228712.738214.1039
49.001-4.0006-0.4785.62581.05230.20980.01770.20410.0351-0.81220.1469-0.6664-0.16920.0461-0.16460.2142-0.00470.10550.1853-0.07420.127958.552322.97262.8659
55.68742.7092-0.38868.6227-4.555110.5975-0.1359-0.28640.38920.45630.77140.7618-0.20140.2724-0.63550.18290.04730.07080.25290.05390.132242.941637.34656.8236
63.2022-2.05054.29215.1833-1.55826.127-0.151-0.4979-0.14840.04370.4130.1817-0.1292-0.604-0.2620.0555-0.04810.02750.1864-0.02290.103648.966928.971117.6931
71.9354-2.4339-2.517910.05833.89093.3509-0.2373-0.25560.22450.13990.5691-0.58670.28230.3552-0.33180.0373-0.0056-0.01080.1864-0.11430.118750.733341.297927.7183
85.9655-3.4008-1.3014.4592.09451.01010.2269-0.7063-0.45230.3633-0.0176-0.25890.2164-0.0546-0.20930.1581-0.0545-0.14190.24310.09850.152841.512636.769438.9492
913.7105-0.58545.72472.4588-0.38511.43110.50880.1884-0.5963-0.4297-0.05690.00620.00040.3605-0.45190.1393-0.0067-0.06960.1277-0.00270.099546.54930.909634.9746
104.7247-0.8921-2.29265.6347-4.38485.3618-0.0905-0.1392-0.0494-1.02210.35290.24270.9184-0.2655-0.26250.1935-0.0642-0.0470.2106-0.0430.0942.351240.315524.1143
114.3163-4.7728-4.23316.95476.6516.47840.5277-0.1580.4594-0.68780.0483-0.6249-0.6097-0.0302-0.5760.158-0.0750.09250.1811-0.05230.134853.978535.766614.1123
121.8008-0.1782-0.48369.8061.1172.6803-0.0060.57320.4773-0.45050.16210.3071-0.08770.0158-0.1560.0943-0.0015-0.00450.2090.15140.147245.547530.04592.8223
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 4
2X-RAY DIFFRACTION2A5 - 8
3X-RAY DIFFRACTION3A9 - 12
4X-RAY DIFFRACTION4A13 - 16
5X-RAY DIFFRACTION5B1 - 4
6X-RAY DIFFRACTION6B5 - 8
7X-RAY DIFFRACTION7B9 - 12
8X-RAY DIFFRACTION8B13 - 16
9X-RAY DIFFRACTION9C1 - 4
10X-RAY DIFFRACTION10C5 - 8
11X-RAY DIFFRACTION11C9 - 12
12X-RAY DIFFRACTION12C13 - 16

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