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

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Basic information

Entry
Database: PDB / ID: 5hnj
TitleBase Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex
ComponentsRNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
KeywordsRNA / 5-formylcytosine
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsLuo, Z.P. / 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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.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

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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*(OFC)P*GP*UP*AP*C)-3')
B: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
C: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
D: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
E: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
F: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3738
Polymers15,3276
Non-polymers462
Water4,522251
1
A: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
B: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1554
Polymers5,1092
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-2 kcal/mol
Surface area3090 Å2
MethodPISA
2
C: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
D: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1092
Polymers5,1092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-2 kcal/mol
Surface area3130 Å2
MethodPISA
3
E: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
F: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')


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-2 kcal/mol
Surface area3090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.692, 45.923, 45.406
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 2554.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 50 mM HEPES Na (pH 7.0), 50 mM MgSO4, 1.6 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 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: 1.24→30 Å / Num. obs: 35304 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 35.4
Reflection shellResolution: 1.24→1.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 197D

197d


Resolution: 1.24→25.2 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.811 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.009 / ESU R Free: 0.008 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15451 1770 5 %RANDOM
Rwork0.13351 ---
obs0.13454 33515 99.88 %-
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: 18.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.23 Å2
2---1.02 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.24→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1014 2 251 1267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0121140
X-RAY DIFFRACTIONr_bond_other_d0.0040.02474
X-RAY DIFFRACTIONr_angle_refined_deg2.1951.4621746
X-RAY DIFFRACTIONr_angle_other_deg1.9431146
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_restr0.1010.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0330.02576
X-RAY DIFFRACTIONr_gen_planes_other0.010.02246
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_it3.8443.4721140
X-RAY DIFFRACTIONr_scbond_other3.8473.4711139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2486.551746
X-RAY DIFFRACTIONr_long_range_B_refined4.71316.7056588
X-RAY DIFFRACTIONr_long_range_B_other4.67416.6496551
X-RAY DIFFRACTIONr_rigid_bond_restr5.84631614
X-RAY DIFFRACTIONr_sphericity_free22.75252
X-RAY DIFFRACTIONr_sphericity_bonded12.88851742
LS refinement shellResolution: 1.239→1.271 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 119 -
Rwork0.224 2415 -
obs--98.45 %

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