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- PDB-5hnq: Base Pairing and Structure Insights into the 5-Formylcytosine in ... -

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Basic information

Entry
Database: PDB / ID: 5hnq
TitleBase Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex
Components5fC modified RNA
KeywordsRNA / 5-formylcytosine
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsLuo, Z. / Sheng, J.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Base pairing and structural insights into the 5-formylcytosine in RNA duplex.
Authors: Wang, R. / Luo, Z. / He, K. / Delaney, M.O. / Chen, D. / Sheng, J.
History
DepositionJan 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5fC modified RNA
B: 5fC modified RNA
C: 5fC modified RNA
D: 5fC modified RNA
E: 5fC modified RNA
F: 5fC modified RNA
G: 5fC modified RNA
H: 5fC modified RNA
I: 5fC modified RNA
J: 5fC modified RNA
K: 5fC modified RNA
L: 5fC modified RNA
M: 5fC modified RNA


Theoretical massNumber of molelcules
Total (without water)33,20913
Polymers33,20913
Non-polymers00
Water1086
1
A: 5fC modified RNA
B: 5fC modified RNA


Theoretical massNumber of molelcules
Total (without water)5,1092
Polymers5,1092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-2 kcal/mol
Surface area3080 Å2
MethodPISA
2
C: 5fC modified RNA
D: 5fC modified RNA


Theoretical massNumber of molelcules
Total (without water)5,1092
Polymers5,1092
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-2 kcal/mol
Surface area3090 Å2
MethodPISA
3
E: 5fC modified RNA
F: 5fC modified RNA


Theoretical massNumber of molelcules
Total (without water)5,1092
Polymers5,1092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-1 kcal/mol
Surface area3060 Å2
MethodPISA
4
G: 5fC modified RNA
H: 5fC modified RNA


Theoretical massNumber of molelcules
Total (without water)5,1092
Polymers5,1092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-0 kcal/mol
Surface area3070 Å2
MethodPISA
5
I: 5fC modified RNA
J: 5fC modified RNA


Theoretical massNumber of molelcules
Total (without water)5,1092
Polymers5,1092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-1 kcal/mol
Surface area3050 Å2
MethodPISA
6
K: 5fC modified RNA
L: 5fC modified RNA


Theoretical massNumber of molelcules
Total (without water)5,1092
Polymers5,1092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-1 kcal/mol
Surface area3090 Å2
MethodPISA
7
M: 5fC modified RNA

M: 5fC modified RNA


Theoretical massNumber of molelcules
Total (without water)5,1092
Polymers5,1092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area730 Å2
ΔGint-2 kcal/mol
Surface area3070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.901, 44.323, 50.586
Angle α, β, γ (deg.)90.00, 102.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain
5fC modified RNA


Mass: 2554.571 Da / Num. of mol.: 13 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% MPD, 40 mM Na cacodylate (pH 6.0), 12 mM Spermine tetrahydrochloride, 80 mM NaCl, 12 mM KCl, 20mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12285 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FC1

5fc1


Resolution: 2.4→28.72 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 20.54 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26109 619 5.2 %RANDOM
Rwork0.22144 ---
obs0.22358 11304 99.69 %-
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: 103.509 Å2
Baniso -1Baniso -2Baniso -3
1-23.51 Å20 Å2-4.45 Å2
2--28.82 Å20 Å2
3----52.33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2197 0 6 2203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4081.4693679
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_restr0.1450.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021079
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_it9.82212.8892443
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.83557.711209
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 29 -
Rwork0.383 829 -
obs--98.96 %
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)
11.3680.05060.36191.43750.28042.71350.2389-0.3272-0.13160.07480.1489-0.4711-0.40780.2967-0.38780.1545-0.0994-0.03470.1802-0.06210.315139.24596.94535.6679
21.145-0.24641.17871.23011.34447.35530.11890.2657-0.4789-0.3028-0.08960.54810.0644-1.1472-0.02930.2466-0.0149-0.10020.59010.00850.52649.39158.405527.8362
30.8374-0.21832.07270.2226-0.785711.8546-0.4572-0.56580.0907-0.0240.2763-0.38030.7962-1.39780.18090.93880.0822-0.07020.7782-0.05021.140851.72821.995176.635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION1B1 - 8
3X-RAY DIFFRACTION1C1 - 8
4X-RAY DIFFRACTION1D1 - 8
5X-RAY DIFFRACTION1E1 - 8
6X-RAY DIFFRACTION1F1 - 8
7X-RAY DIFFRACTION2G1 - 8
8X-RAY DIFFRACTION2H1 - 8
9X-RAY DIFFRACTION2I1 - 8
10X-RAY DIFFRACTION2J1 - 8
11X-RAY DIFFRACTION2K1 - 8
12X-RAY DIFFRACTION2L1 - 8
13X-RAY DIFFRACTION3M1 - 8

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