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- PDB-4isj: RNA Ligase RtcB in complex with Mn(II) -

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Basic information

Entry
Database: PDB / ID: 4isj
TitleRNA Ligase RtcB in complex with Mn(II)
ComponentstRNA-splicing ligase RtcB
KeywordsLIGASE / RNA ligase
Function / homology
Function and homology information


RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / : / tRNA-splicing ligase complex / GMP binding / RNA ligase (ATP) activity / intein-mediated protein splicing / intron homing / manganese ion binding / endonuclease activity ...RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / : / tRNA-splicing ligase complex / GMP binding / RNA ligase (ATP) activity / intein-mediated protein splicing / intron homing / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / GTP binding / DNA binding
Similarity search - Function
tRNA-splicing ligase RtcB / tRNA-splicing ligase RtcB / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. ...tRNA-splicing ligase RtcB / tRNA-splicing ligase RtcB / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
sucrose / : / tRNA-splicing ligase RtcB
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.344 Å
AuthorsDesai, K.K. / Bingman, C.A. / Phillips Jr., G.N. / Raines, R.T.
CitationJournal: Biochemistry / Year: 2013
Title: Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation.
Authors: Desai, K.K. / Bingman, C.A. / Phillips, G.N. / Raines, R.T.
History
DepositionJan 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA-splicing ligase RtcB
B: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,20819
Polymers107,1652
Non-polymers2,04317
Water7,494416
1
A: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,65210
Polymers53,5821
Non-polymers1,0709
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5569
Polymers53,5821
Non-polymers9748
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-173 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.038, 137.704, 149.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein tRNA-splicing ligase RtcB / Pho hyp2 intein


Mass: 53582.418 Da / Num. of mol.: 2 / Fragment: mature RtcB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: ATCC 700860 / Gene: PH1602, rtcB / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O59245, Ligases; Forming phosphoric-ester bonds, Hydrolases; Acting on ester bonds
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE REFERENCE SEQUENCE IS O59245 (RTCB_PYRHO); HOWEVER, THIS SEQUENCE CONTAINS AN INTEIN WHICH IS ...THE REFERENCE SEQUENCE IS O59245 (RTCB_PYRHO); HOWEVER, THIS SEQUENCE CONTAINS AN INTEIN WHICH IS SPLICED OUT IN THE MATURE RTCB. THE COMPLETE SEQUENCE IS: MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG

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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: 3.88 Å3/Da / Density % sol: 68.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Crystals were grown from one part RtcB solution at 200 micromolar, mixed with one part reservoir solution, 2.1 M ammonium sulfate, 0.1 M bistris buffer. Crystals were cryoprotected in ...Details: Crystals were grown from one part RtcB solution at 200 micromolar, mixed with one part reservoir solution, 2.1 M ammonium sulfate, 0.1 M bistris buffer. Crystals were cryoprotected in reservoir solution supplemented with 20% sucrose., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2012
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.344→49.49 Å / Num. all: 70213 / Num. obs: 70143 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Net I/σ(I): 12.2
Reflection shellResolution: 2.35→2.39 Å / % possible all: 96.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.344→49.49 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 18.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 2148 3.06 %randomly selected in thin shells
Rwork0.1564 ---
all0.1576 70213 --
obs0.1576 70139 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.344→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7518 0 113 416 8047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137772
X-RAY DIFFRACTIONf_angle_d1.5110504
X-RAY DIFFRACTIONf_dihedral_angle_d16.0042912
X-RAY DIFFRACTIONf_chiral_restr0.1351120
X-RAY DIFFRACTIONf_plane_restr0.0061366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.344-2.3980.24291400.19234060X-RAY DIFFRACTION90
2.398-2.4580.24441480.1894507X-RAY DIFFRACTION100
2.458-2.52450.24451240.18894523X-RAY DIFFRACTION100
2.5245-2.59870.22951500.17844471X-RAY DIFFRACTION99
2.5987-2.68260.21691390.17084495X-RAY DIFFRACTION100
2.6826-2.77850.21181460.17284525X-RAY DIFFRACTION100
2.7785-2.88970.2371460.16624511X-RAY DIFFRACTION99
2.8897-3.02120.21581360.16614533X-RAY DIFFRACTION100
3.0212-3.18050.20241410.16824523X-RAY DIFFRACTION100
3.1805-3.37970.21481480.16274567X-RAY DIFFRACTION100
3.3797-3.64060.18861410.14784580X-RAY DIFFRACTION100
3.6406-4.00680.16391560.13524563X-RAY DIFFRACTION100
4.0068-4.58620.15771200.11934645X-RAY DIFFRACTION100
4.5862-5.77670.17991750.13664635X-RAY DIFFRACTION100
5.7767-49.50310.16091380.17624853X-RAY DIFFRACTION100

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