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- PDB-6tzo: Crystal Structure of Fungal RNA Kinase -

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Basic information

Entry
Database: PDB / ID: 6tzo
TitleCrystal Structure of Fungal RNA Kinase
ComponentstRNA ligase
KeywordsTRANSFERASE / RNA ligase / RNA repair / polynucleotide kinase
Function / homology
Function and homology information


GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / RNA ligase (ATP) / RNA ligase (ATP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / phosphoric diester hydrolase activity / endonuclease activity / ATP binding / nucleus
Similarity search - Function
tRNA ligase Trl1, fungi / tRNA ligase, phosphodiesterase / tRNA ligase, kinase domain, fungi / Fungal tRNA ligase phosphodiesterase domain / tRNA ligase kinase domain / T4 RNA ligase 1, N-terminal / RNA ligase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / tRNA ligase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsShuman, S. / Goldgur, Y. / Banerjee, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM42498 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.
Authors: Banerjee, A. / Goldgur, Y. / Schwer, B. / Shuman, S.
History
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0673
Polymers49,5451
Non-polymers5222
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.141, 56.427, 82.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein tRNA ligase


Mass: 49544.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876
Gene: LIG1, RLG1, TRL1, CAALFM_C702060WA, CaJ7.0238, CaO19.13864, CaO19.6511
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P43075, RNA ligase (ATP)
#2: Chemical ChemComp-DGI / 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE


Type: DNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15M NaH2PO4, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 25854 / % possible obs: 97.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Rrim(I) all: 0.064 / Χ2: 1.481 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7340.52410290.8030.2690.5921.07877
1.73-1.764.30.51911160.8080.2570.5811.14886.8
1.76-1.794.30.44812140.8440.2260.5051.16692.5
1.79-1.834.90.40912620.9030.1940.4551.19297.9
1.83-1.875.80.34512950.9490.1520.3771.22199.8
1.87-1.9160.3113060.9480.1350.3391.21699.8
1.91-1.966.20.26313080.9650.1140.2871.30399.5
1.96-2.026.20.21813050.9760.0940.2381.33399.4
2.02-2.076.30.18912990.9820.080.2051.36599.8
2.07-2.145.80.15212980.9860.0680.1671.53199.8
2.14-2.225.80.13713230.9860.0620.1511.56899.8
2.22-2.316.50.11312950.9930.0480.1231.69299.7
2.31-2.416.50.113240.9930.0430.1091.68399.8
2.41-2.546.40.08913260.9940.0380.0971.76399.7
2.54-2.76.10.07813330.9950.0340.0851.83299.9
2.7-2.915.90.06913100.9950.030.0751.88599.1
2.91-3.26.50.05613390.9970.0230.0611.78199.8
3.2-3.666.30.04613400.9970.020.051.65599.6
3.66-4.615.90.03713770.9980.0160.041.41299.6
4.61-505.90.03314550.9990.0140.0361.14999

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5u32

5u32


Resolution: 1.69→46.575 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.91
RfactorNum. reflection% reflection
Rfree0.209 2000 7.75 %
Rwork0.1804 --
obs0.1826 25803 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.16 Å2 / Biso mean: 38.5464 Å2 / Biso min: 15.37 Å2
Refinement stepCycle: final / Resolution: 1.69→46.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 32 170 2034
Biso mean--29.95 42.72 -
Num. residues----224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.699-1.74130.28781130.264134478
1.7413-1.78830.30021330.2551157491
1.7883-1.8410.27291390.223166598
1.841-1.90040.23521440.21211715100
1.9004-1.96830.24921450.1954172299
1.9683-2.04710.22911420.19911699100
2.0471-2.14030.25521450.18721719100
2.1403-2.25310.25341460.19651742100
2.2531-2.39430.23981460.18461737100
2.3943-2.57910.24341460.19251730100
2.5791-2.83870.19641460.1947174899
2.8387-3.24930.22761480.18121754100
3.2493-4.09340.18121500.16531782100
4.0934-46.50.16391570.1535187299
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)
13.86170.83430.1141.981-0.7912.8613-0.09530.07790.0272-0.03990.13030.12120.0991-0.36340.01260.1531-0.00550.00140.17440.00530.1296-44.99879.164793.2324
23.46352.7425-0.86084.2023-0.60050.8948-0.0319-0.2619-0.09670.1565-0.0057-0.02350.0888-0.04290.0420.24630.0202-0.03730.20740.01940.1316-43.67375.9968103.4539
38.291-0.54993.61892.0969-0.00098.4121-0.38560.23740.9504-0.2190.0181-0.5247-0.57060.29640.27110.2691-0.0626-0.03250.18-0.00750.4038-27.094325.786794.685
46.66750.3581-1.69479.22740.63462.16240.02620.63721.0921-0.8188-0.0232-0.1447-0.6791-0.48020.07320.37670.0432-0.03370.3355-0.03110.4898-37.812129.634196.0497
52.4195-0.2999-0.61461.4044-0.00961.5084-0.0545-0.068-0.1760.1430.0448-0.21530.05660.06570.00390.19270.0353-0.04280.186-0.01120.2123-29.88788.095497.6254
63.90412.722-1.63426.4945-3.30226.6386-0.34770.8126-0.2159-0.63490.3014-0.02880.4034-0.17130.04190.2208-0.02930.05730.3907-0.11980.2356-33.98286.095481.6944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 408 through 479 )A408 - 479
2X-RAY DIFFRACTION2chain 'A' and (resid 480 through 517 )A480 - 517
3X-RAY DIFFRACTION3chain 'A' and (resid 518 through 532 )A518 - 532
4X-RAY DIFFRACTION4chain 'A' and (resid 533 through 557 )A533 - 557
5X-RAY DIFFRACTION5chain 'A' and (resid 558 through 604 )A558 - 604
6X-RAY DIFFRACTION6chain 'A' and (resid 605 through 630 )A605 - 630

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