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- PDB-7lfq: Pyrococcus RNA ligase -

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Basic information

Entry
Database: PDB / ID: 7lfq
TitlePyrococcus RNA ligase
Components
  • DNA (5'-D(*AP*TP*GP*TP*CP*C)-3')
  • RNA-splicing ligase RtcB
KeywordsLIGASE/DNA / RNA repair / LIGASE / LIGASE-DNA complex
Function / homology
Function and homology information


RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / RNA ligase (ATP) activity / intron homing / intein-mediated protein splicing / tRNA processing / GMP binding / manganese ion binding / endonuclease activity ...RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / RNA ligase (ATP) activity / intron homing / intein-mediated protein splicing / tRNA processing / GMP binding / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / GTP binding / DNA binding
Similarity search - Function
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 ...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. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily
Similarity search - Domain/homology
: / DNA / tRNA-splicing ligase RtcB
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGoldgur, Y. / Shuman, S. / Banerjee, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
CitationJournal: Rna / Year: 2021
Title: Structure of 3'-PO 4 /5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide.
Authors: Banerjee, A. / Goldgur, Y. / Shuman, S.
History
DepositionJan 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jun 29, 2022Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num
Revision 2.1Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-splicing ligase RtcB
B: DNA (5'-D(*AP*TP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7214
Polymers57,5862
Non-polymers1352
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.379, 151.379, 82.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

#1: Protein RNA-splicing ligase RtcB / 3'-phosphate/5'-hydroxy nucleic acid ligase


Mass: 55801.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: rtcB, PH1602
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O59245, 3'-phosphate/5'-hydroxy nucleic acid ligase, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(*AP*TP*GP*TP*CP*C)-3')


Mass: 1784.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Morpheus G6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 26802 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 67.81 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.026 / Rrim(I) all: 0.088 / Χ2: 1.055 / Net I/σ(I): 8.2 / Num. measured all: 293064
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.7511.11.31113110.7430.4111.3750.972100
2.75-2.8111.08512910.7990.3421.1380.963100
2.8-2.8510.80.91513270.8370.2920.9610.985100
2.85-2.9110.60.79513100.870.2550.8361.01100
2.91-2.97100.62813240.9230.2080.6621.015100
2.97-3.049.10.48413070.9360.1680.5131.011100
3.04-3.129.10.40513120.9630.140.4291.029100
3.12-3.210.90.33613350.9770.1060.3531.031100
3.2-3.3120.25813260.9860.0770.271.062100
3.3-3.412.20.20713070.9910.0620.2161.096100
3.4-3.52120.16213420.9950.0490.1691.156100
3.52-3.66120.11413250.9970.0340.1191.151100
3.66-3.8311.90.09213360.9980.0280.0961.165100
3.83-4.0311.70.0713350.9990.0210.0731.182100
4.03-4.2911.60.05313420.9990.0160.0551.09799.9
4.29-4.6211.20.04313440.9990.0130.0451.052100
4.62-5.0810.80.0413710.9990.0120.0421.04100
5.08-5.819.30.04313680.9990.0150.0461.09100
5.81-7.3210.50.035138710.0110.0371.018100
7.32-5010.80.024150210.0080.0250.913100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
PHENIX1.18.2_3874+SVNrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWR

4dwr


Resolution: 2.7→47.87 Å / SU ML: 0.3218 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2161 2000 7.48 %
Rwork0.1912 24752 -
obs0.1931 26752 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 118 6 17 3910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01093981
X-RAY DIFFRACTIONf_angle_d1.35135397
X-RAY DIFFRACTIONf_chiral_restr0.0625575
X-RAY DIFFRACTIONf_plane_restr0.0088689
X-RAY DIFFRACTIONf_dihedral_angle_d22.4431595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.31671390.30311720X-RAY DIFFRACTION99.84
2.77-2.840.30991400.28021733X-RAY DIFFRACTION100
2.84-2.930.3281400.26221742X-RAY DIFFRACTION100
2.93-3.020.28421410.24461744X-RAY DIFFRACTION99.95
3.02-3.130.26061400.23641725X-RAY DIFFRACTION100
3.13-3.260.251420.23331758X-RAY DIFFRACTION100
3.26-3.40.25691410.22061733X-RAY DIFFRACTION100
3.4-3.580.24661420.22091778X-RAY DIFFRACTION100
3.58-3.810.23621410.20151741X-RAY DIFFRACTION100
3.81-4.10.20281440.18131779X-RAY DIFFRACTION100
4.1-4.510.17041430.1591763X-RAY DIFFRACTION100
4.52-5.170.18961450.15451797X-RAY DIFFRACTION100
5.17-6.510.20421470.18561812X-RAY DIFFRACTION100
6.51-47.870.181550.16031927X-RAY DIFFRACTION99.95
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)
12.885039288130.6091265960270.5012926985792.271436861290.4242867724251.64812799206-0.0692621002235-0.1367200673170.479529693624-0.1205386828190.01538688784550.034738125715-0.42810375317-0.0739902475350.1245444132870.4389457178070.113972226603-0.02065069788810.4463977262110.06307829642040.4538485446752.414173919725.453836169918.4404800407
26.65079448242-2.38201993576-0.7785908536581.734644368952.246175679174.707856670940.3319362748310.337707715540.82659390084-0.6535264259730.2022625998710.849164143382-0.522751714626-1.58001819868-0.578147016260.5617500321570.0427721560706-0.01066326988690.9450488014960.03575689827021.0211441989725.050994144417.94383637412.1801073918
33.79180711271-0.500128824467-1.524024571853.424665290640.9588851392873.44882133697-0.0696155318054-0.173982632802-0.0410209716950.2288643243530.01529278484560.6013557790860.144544679937-0.4783252221750.09241821056080.4126284747490.0288308867643-0.04336623483680.50618850870.04125830311650.45271750356837.523380408913.897041233413.4569762538
42.051071980980.1674451756790.321619150553.356568598210.5288312921632.48691792917-0.0472606634446-0.5200564036140.8677964829470.207937235830.2074418015810.26363730091-0.709362565765-0.442443466798-0.01012041566860.5109872498240.2123539909280.07606761385240.6708859896530.01152918897720.74903635927339.898871932428.376620433822.0035754599
52.928584553620.5373875551240.7373665961663.288995912712.002103870834.31446182010.0445821021846-0.1169073219180.004961329837090.0671779022776-0.1013763591290.460202113922-0.0205077615782-0.3215702527790.07019801563860.3179951648640.05016798849210.06358820167020.4929704268460.08706872626590.47711197922141.828232976212.736476904118.1040683499
63.694593573341.13617999678-0.9219141218311.704611570131.670908471373.00867507668-0.131945597202-0.01982489229350.316514514851-0.2644665034940.1152031135990.442748157037-0.553700331537-0.06267508236410.0229386719160.5158286268710.115157566727-0.04804057000450.4307964936590.001209777079570.46764768931153.905857791620.206246343517.1994077273
73.29096416622-0.2656198184591.517275154332.375975961430.4019477479753.2293293460.02153404191080.7597251078340.708487514446-0.727217807089-0.075906751198-0.0024420388751-0.3000675430680.3742640164290.04965724899810.7302529364080.03281657312370.04593858341750.6669456455320.1514676642460.68049406148552.005487429122.40698036120.627089854572
81.88730187791-0.6223637069382.734003925558.49352657255-5.821838694546.86550372423-1.242800189550.06402160874952.03937012170.5340402038431.72028299632.00873207445-1.123957695520.31107475079-0.4710460020431.336866055080.263020135869-0.4771347610041.47908647892-0.1369729737791.9988728311334.283251187635.61654914998.89879432989
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 126 )AA1 - 1261 - 126
22chain 'A' and (resid 127 through 157 )AA127 - 157127 - 157
33chain 'A' and (resid 158 through 221 )AA158 - 221158 - 221
44chain 'A' and (resid 222 through 275 )AA222 - 275222 - 275
55chain 'A' and (resid 276 through 384 )AA276 - 384276 - 384
66chain 'A' and (resid 385 through 413 )AA385 - 413385 - 413
77chain 'A' and (resid 414 through 481 )AA414 - 481414 - 481
88chain 'B' and (resid 1 through 6 )BB1 - 6

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