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- PDB-6u05: Crystal Structure of Fungal RNA Kinase -

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Basic information

Entry
Database: PDB / ID: 6u05
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 / phosphorylation / 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
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / tRNA ligase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 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 13, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1084
Polymers49,5461
Non-polymers5623
Water3,027168
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)77.747, 44.690, 79.500
Angle α, β, γ (deg.)90.000, 93.530, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein tRNA ligase


Mass: 49545.871 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-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M KH2PO4, 20% PEG3350 / Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.948→50 Å / Num. obs: 38436 / % possible obs: 96.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.037 / Rrim(I) all: 0.078 / Χ2: 1.387 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.982.70.55616520.8630.3560.6631.18183.1
1.98-2.022.80.54417340.8640.3460.6481.09387.4
2.02-2.0630.51418050.8350.3240.6111.14793.2
2.06-2.13.10.46819140.8930.2930.5551.15996.3
2.1-2.153.30.38719110.940.2370.4561.17595.6
2.15-2.23.50.40618450.9390.2380.4741.21594.3
2.2-2.254.10.36119320.9640.1950.4121.21697.7
2.25-2.314.30.30319650.9760.1590.3431.23299.3
2.31-2.384.30.28119670.9750.1460.3181.26998.9
2.38-2.464.30.21819720.9840.1140.2471.2999
2.46-2.544.30.19719610.9820.1030.2241.28599.3
2.54-2.654.20.15219640.990.0810.1731.31298.5
2.65-2.7740.12519640.990.0690.1431.31297.8
2.77-2.914.20.10418770.9920.0550.1181.41894.8
2.91-3.14.40.08319910.9960.0430.0941.53499.4
3.1-3.334.40.06819800.9960.0350.0771.67899.4
3.33-3.674.20.05520110.9970.0290.0621.81299.5
3.67-4.240.04318980.9980.0230.0491.83694.7
4.2-5.294.40.03620410.9990.0180.0411.60899.9
5.29-504.10.03220520.9990.0170.0371.39497.3

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
SOLOMONphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U32

5u32


Resolution: 1.948→39.675 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.01
RfactorNum. reflection% reflection
Rfree0.2213 2011 5.24 %
Rwork0.1852 --
obs0.187 38346 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.93 Å2 / Biso mean: 52.7025 Å2 / Biso min: 21.42 Å2
Refinement stepCycle: final / Resolution: 1.948→39.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 34 168 3549
Biso mean--37.63 48.81 -
Num. residues----413
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9483-1.99710.38451110.3165193072
1.9971-2.05110.33161350.2869242490
2.0511-2.11140.31171440.2559257795
2.1114-2.17960.31251450.2408253794
2.1796-2.25740.29811500.2229263097
2.2574-2.34780.24961400.2128270499
2.3478-2.45470.2361470.2057265799
2.4547-2.58410.21371320.1958268099
2.5841-2.74590.24611640.1984269199
2.7459-2.95790.22161480.1941259696
2.9579-3.25540.2431490.1837272799
3.2554-3.72620.1981530.1739273199
3.7262-4.69340.18411400.148265496
4.6934-39.670.18381530.1669279798
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)
14.8886-0.7788-2.46411.98730.34263.1656-0.1619-0.0928-0.05610.00570.0793-0.04550.1455-0.01970.06190.3106-0.0420.02380.2211-0.05190.286824.55696.71219.1603
20.4265-0.2883-0.00250.19110.00270.0272-0.1362-0.07510.26720.06150.25880.5542-0.3627-0.3089-0.12690.55960.0634-0.06030.64280.22490.904143.5064-14.760523.9033
33.1448-0.4573-0.61132.14630.47863.17110.02520.2694-0.0203-0.2090.01240.228-0.164-0.4605-0.05440.27260.017-0.01050.27510.04180.265671.3023-27.10927.32
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 409 through 626 )A409 - 626
2X-RAY DIFFRACTION2chain 'A' and (resid 627 through 653 )A627 - 653
3X-RAY DIFFRACTION3chain 'A' and (resid 654 through 832 )A654 - 832

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