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- PDB-4nfq: Crystal Structure Analysis of the 16mer GCAGNCUUAAGUCUGC containi... -

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Basic information

Entry
Database: PDB / ID: 4nfq
TitleCrystal Structure Analysis of the 16mer GCAGNCUUAAGUCUGC containing 7-triazolyl-8-aza-7-deazaadenosine
ComponentsGCAG(7AT)CUUAAGUCUGC
KeywordsRNA / RNA 16mer oligo / 7-triazolyl-8-aza-7-deazaadenosine / Position 5
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCAG(7AT)CUUAAGUCUGC
B: GCAG(7AT)CUUAAGUCUGC
C: GCAG(7AT)CUUAAGUCUGC


Theoretical massNumber of molelcules
Total (without water)15,4953
Polymers15,4953
Non-polymers00
Water1,40578
1
A: GCAG(7AT)CUUAAGUCUGC

A: GCAG(7AT)CUUAAGUCUGC


Theoretical massNumber of molelcules
Total (without water)10,3302
Polymers10,3302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area1510 Å2
ΔGint-10 kcal/mol
Surface area5930 Å2
MethodPISA
2
B: GCAG(7AT)CUUAAGUCUGC
C: GCAG(7AT)CUUAAGUCUGC


Theoretical massNumber of molelcules
Total (without water)10,3302
Polymers10,3302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-10 kcal/mol
Surface area5920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.360, 44.380, 48.830
Angle α, β, γ (deg.)90.00, 121.97, 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 GCAG(7AT)CUUAAGUCUGC


Mass: 5165.129 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% MPD(v/v) (Drop), 20% MPD(v/v) (reservoir), 40mM Na-cacodylate trihydrate (pH 7), 12mM spermine tetrahydrochloride, 80mM KCl, 10mM 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: 1.127 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2013
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: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.7→36.79 Å / Num. all: 15661 / Num. obs: 14671 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.88 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 16.42
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 1.69 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.27 / Num. unique all: 1133 / % possible all: 88.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.79 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.975 / SU B: 8.393 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24351 740 5 %RANDOM
Rwork0.2227 ---
all0.22383 14671 --
obs0.22383 13931 94.08 %-
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: 38.673 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å20 Å2-1.73 Å2
2--3.04 Å20 Å2
3----2.57 Å2
Refine analyzeLuzzati coordinate error free: 0.121 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1026 0 78 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121146
X-RAY DIFFRACTIONr_bond_other_d0.0090.02474
X-RAY DIFFRACTIONr_angle_refined_deg2.5031.4081779
X-RAY DIFFRACTIONr_angle_other_deg3.4231149
X-RAY DIFFRACTIONr_chiral_restr0.1140.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02573
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02249
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
11A939
12B939
21A939
22C939
31B938
32C938
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 53 -
Rwork0.374 949 -
obs-949 88.83 %
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)
12.07740.2565-0.45997.4809-3.67095.5927-0.13960.10590.1658-0.47650.35260.75290.224-0.6587-0.21290.0650.00570.02160.24010.11720.32761.237322.068934.7008
22.3645-1.2825-0.83689.35355.11862.81810.17020.3787-0.0011-0.3764-0.0347-0.1317-0.242-0.031-0.13550.1889-0.00480.06080.12660.04230.2671.0321.334124.2589
34.29941.52092.11141.6241-0.39092.23970.1640.103-0.4819-0.06890.1452-0.05760.1629-0.018-0.30930.1374-0.0078-0.06290.1793-0.03860.261961.018413.517113.9046
410.6638-0.93920.36656.4683-1.01240.78040.06270.32670.3016-0.49130.2853-0.4757-0.0690.0616-0.3480.0728-0.03630.13590.1171-0.08420.332360.059823.37652.5008
53.6192-1.1276-2.32343.5229-3.348114.47180.2225-0.01170.55490.44610.05380.6981-0.8971-0.226-0.27620.10870.05540.16990.21350.02450.516644.787938.01276.6951
68.46561.23424.6532.35391.67923.0229-0.1807-0.5877-0.04770.50170.2927-0.0980.1484-0.1639-0.11210.20190.03380.07320.31720.0280.27350.22529.935817.177
72.1779-1.8649-1.72435.85381.49291.38860.1127-0.14490.35870.06290.1563-0.4529-0.02120.0824-0.2690.1702-0.04090.01240.1968-0.0770.236951.973142.395327.568
86.5242-2.2832-1.750612.7501-1.20431.73440.2957-0.4014-0.48190.4433-0.08240.03980.04150.0039-0.21330.0832-0.0457-0.11190.10480.01990.252942.921238.336238.9466
93.98740.56134.16974.53882.304210.22340.17970.6744-0.81850.0970.1575-0.19440.45090.65-0.33720.20540.0381-0.10610.1898-0.09310.374447.889732.437734.7148
105.85153.9649-4.21656.8878-3.76563.24020.04660.16870.1049-0.73960.08620.12910.1342-0.125-0.13280.1581-0.0312-0.04260.2112-0.04160.250443.622841.247824.2593
115.3431-3.5571-0.80563.36922.3673.50010.1173-0.20540.4033-0.09820.2322-0.4509-0.05080.0939-0.34950.082-0.04120.12960.2252-0.05840.255455.423936.565513.913
129.2759-2.30771.80511.0173-0.3582.09750.20210.49810.172-0.07590.25620.57290.0089-0.1445-0.45830.02050.01050.04010.12410.08560.237947.390130.7852.4841
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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