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- PDB-6u03: Crystal Structure of Fungal RNA Kinase -

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Basic information

Entry
Database: PDB / ID: 6u03
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
GUANOSINE-5'-TRIPHOSPHATE / tRNA ligase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 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

Downloads & links

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Assembly

Deposited unit
A: tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7253
Polymers27,1771
Non-polymers5472
Water2,846158
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)50.227, 55.667, 81.795
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: 27177.484 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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15M NaH2PO4, 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-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 20105 / % possible obs: 99.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.036 / Rrim(I) all: 0.085 / Χ2: 1.667 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.883.90.4579180.7540.2480.5220.9592.3
1.88-1.924.40.449600.8470.2250.4960.92296.9
1.92-1.954.80.4039710.9190.1970.451.01898.9
1.95-1.995.20.389930.9030.1790.4211.1299.5
1.99-2.045.40.3489830.9360.1630.3851.20199.5
2.04-2.085.40.31510080.9420.1490.351.38299.5
2.08-2.145.10.2689930.9360.1330.3011.48699.4
2.14-2.195.40.2519960.9590.1180.2781.53199.6
2.19-2.266.40.2289820.9640.0980.2491.54499.9
2.26-2.336.40.19510000.9780.0840.2121.606100
2.33-2.416.30.17210270.9820.0750.1881.76799.6
2.41-2.516.30.1519990.9840.0660.1651.70199.8
2.51-2.6360.139900.9870.0580.1431.8999.8
2.63-2.765.80.1110230.9910.050.1211.94599.6
2.76-2.945.50.09410100.990.0450.1052.09699.7
2.94-3.164.80.07410090.9910.0380.0832.30199.1
3.16-3.4860.05710240.9980.0260.0622.129100
3.48-3.995.80.04410420.9980.020.0482.118100
3.99-5.025.40.03410560.9980.0160.0381.83299.7
5.02-504.90.03511210.9980.0170.0392.04599.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U32

5u32


Resolution: 1.849→46.02 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.14
RfactorNum. reflection% reflection
Rfree0.215 2000 9.97 %
Rwork0.1696 --
obs0.1742 20059 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.08 Å2 / Biso mean: 34.1717 Å2 / Biso min: 14.17 Å2
Refinement stepCycle: final / Resolution: 1.849→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 33 158 1961
Biso mean--28.2 40.78 -
Num. residues----216
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8485-1.89470.28431290.2146116592
1.8947-1.9460.26391410.2048127198
1.946-2.00320.23281410.1964127499
2.0032-2.06790.22791400.18981270100
2.0679-2.14180.21791430.1721128599
2.1418-2.22760.24251400.17971269100
2.2276-2.32890.21811420.17491278100
2.3289-2.45170.22971420.17521285100
2.4517-2.60530.23571450.18171311100
2.6053-2.80640.25291440.18281292100
2.8064-3.08880.2261440.1837130199
3.0888-3.53560.19891450.17061316100
3.5356-4.45390.18041480.13841329100
4.4539-46.020.19821560.15891413100
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)
10.8566-0.25040.09670.2009-0.43680.8327-0.14350.0547-0.0304-0.03350.12580.02680.1027-0.05940.00010.1979-0.01810.02010.1833-0.00170.1719-39.71396.792191.5217
20.39740.0958-0.07550.4396-0.29960.2203-0.07230.18810.1282-0.1698-0.05170.3616-0.2303-0.30690.00010.23770.0599-0.03110.2456-0.03770.2656-48.883213.276390.9681
30.58330.1173-0.53710.5974-0.66560.8464-0.08190.0439-0.0023-0.11910.11860.10960.1082-0.34590.00010.1989-0.0359-0.01030.26180.01650.1807-48.10247.122894.3776
40.3659-0.396-0.16980.5271-0.0080.15720.0688-0.20060.0497-0.0177-0.14390.37240.17930.01460.00010.24990.03040.03070.22610.00370.2075-49.15497.3454105.2584
50.42070.13850.08640.7748-0.38650.1507-0.2316-0.3066-0.4094-0.14310.0836-0.52060.1377-0.0138-0.03020.2111-0.02710.00130.20110.01390.169-38.22064.362699.9281
60.3142-0.234-0.30240.40110.0840.2647-0.29280.09050.4664-0.2450.0671-0.3637-0.46530.1753-0.00110.3169-0.0544-0.04940.2187-0.00250.2889-27.883426.271493.7963
71.0102-0.3154-0.10080.45110.62320.75210.0443-0.26560.3301-0.15870.0345-0.2064-0.10150.0458-0.00020.2422-0.005-0.02360.2001-0.02270.3099-35.333223.3241102.7036
80.4261-0.4080.40320.7467-0.33940.20870.06510.04680.10390.0620.06020.03660.01190.0843-0.00180.16570.00390.00270.20350.00620.24-27.99949.282195.5739
90.54970.1252-0.45320.0725-0.14750.3794-0.0930.1798-0.2748-0.1709-0.044-0.28030.36520.0693-0.00560.26130.0140.01890.2285-0.05820.211-31.252-0.129488.1106
100.72730.7053-0.08560.65180.05740.45080.20061.02940.2799-0.5414-0.2048-0.0056-0.1899-0.1167-0.00250.238-0.00470.04730.35260.03040.2195-32.931212.300778.1468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 407 through 435 )A407 - 435
2X-RAY DIFFRACTION2chain 'A' and (resid 436 through 454 )A436 - 454
3X-RAY DIFFRACTION3chain 'A' and (resid 455 through 479 )A455 - 479
4X-RAY DIFFRACTION4chain 'A' and (resid 480 through 497 )A480 - 497
5X-RAY DIFFRACTION5chain 'A' and (resid 498 through 517 )A498 - 517
6X-RAY DIFFRACTION6chain 'A' and (resid 518 through 541 )A518 - 541
7X-RAY DIFFRACTION7chain 'A' and (resid 542 through 568 )A542 - 568
8X-RAY DIFFRACTION8chain 'A' and (resid 569 through 588 )A569 - 588
9X-RAY DIFFRACTION9chain 'A' and (resid 589 through 614 )A589 - 614
10X-RAY DIFFRACTION10chain 'A' and (resid 615 through 630 )A615 - 630

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