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- PDB-6u00: Crystal Structure of Fungal RNA Kinase -

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Basic information

Entry
Database: PDB / ID: 6u00
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
PHOSPHATE ION / tRNA ligase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 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 / 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
B: tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2824
Polymers99,0922
Non-polymers1902
Water3,027168
1
A: tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6412
Polymers49,5461
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6412
Polymers49,5461
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.436, 122.873, 150.618
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 409 through 437 or resid 439...
21(chain B and (resid 409 through 437 or resid 439...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 409 through 437 or resid 439...A409 - 437
121(chain A and (resid 409 through 437 or resid 439...A439 - 448
131(chain A and (resid 409 through 437 or resid 439...A451 - 480
141(chain A and (resid 409 through 437 or resid 439...A482 - 495
151(chain A and (resid 409 through 437 or resid 439...A497 - 530
161(chain A and (resid 409 through 437 or resid 439...A544
171(chain A and (resid 409 through 437 or resid 439...A546
181(chain A and (resid 409 through 437 or resid 439...A548 - 572
191(chain A and (resid 409 through 437 or resid 439...A596 - 626
1101(chain A and (resid 409 through 437 or resid 439...A628
1111(chain A and (resid 409 through 437 or resid 439...A628
1121(chain A and (resid 409 through 437 or resid 439...A800
211(chain B and (resid 409 through 437 or resid 439...B409 - 437
221(chain B and (resid 409 through 437 or resid 439...B439 - 448
231(chain B and (resid 409 through 437 or resid 439...B451 - 480
241(chain B and (resid 409 through 437 or resid 439...B544
251(chain B and (resid 409 through 437 or resid 439...B544
261(chain B and (resid 409 through 437 or resid 439...B0
271(chain B and (resid 409 through 437 or resid 439...B548 - 572
281(chain B and (resid 409 through 437 or resid 439...B5
291(chain B and (resid 409 through 437 or resid 439...B0
2101(chain B and (resid 409 through 437 or resid 439...B62
2111(chain B and (resid 409 through 437 or resid 439...B800

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Components

#1: Protein tRNA ligase


Mass: 49545.871 Da / Num. of mol.: 2
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: 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 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: 1.75 Å3/Da / Density % sol: 29.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.3M NaH2PO4, 15%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: 1.98→50 Å / Num. obs: 34731 / % possible obs: 95.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Χ2: 1.376 / Net I/σ(I): 10.5 / Num. measured all: 211528
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.015.40.61812810.8420.2690.6760.9373.7
2.01-2.055.70.53614470.8750.2280.5840.93780.2
2.05-2.095.80.44515150.9190.1890.4850.95685.7
2.09-2.135.90.39515930.9310.1660.4290.99488.2
2.13-2.185.90.33617060.9550.1420.3661.04895.8
2.18-2.2360.29817740.9660.1260.3241.08798.7
2.23-2.296.20.25717820.9730.1090.281.12199.3
2.29-2.356.30.24117790.9790.1030.2621.13699.8
2.35-2.426.20.21518020.9790.0940.2351.17899.6
2.42-2.495.70.17617960.9830.0810.1941.23199.7
2.49-2.5860.14817880.9890.0650.1621.31899.2
2.58-2.696.90.12417950.9930.0510.1341.413100
2.69-2.816.80.1118370.9930.0460.1191.53699.9
2.81-2.966.60.09117850.9950.0380.0991.63999.8
2.96-3.146.40.06918020.9960.030.0761.75699.6
3.14-3.396.10.05518170.9970.0250.061.89199.2
3.39-3.735.30.04518040.9970.0220.0511.85798.3
3.73-4.266.30.03718320.9980.0160.0411.79399.6
4.26-5.376.10.03218450.9990.0150.0351.6399.2
5.37-505.80.02919510.9990.0130.0321.54399.1

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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: 1.981→47.907 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1998 5.76 %
Rwork0.1926 32692 -
obs0.1951 34690 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.72 Å2 / Biso mean: 60.127 Å2 / Biso min: 27.01 Å2
Refinement stepCycle: final / Resolution: 1.981→47.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 10 168 3629
Biso mean--93.38 48.68 -
Num. residues----421
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1130X-RAY DIFFRACTION1.762TORSIONAL
12B1130X-RAY DIFFRACTION1.762TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.981-2.03010.34781100.2634180376
2.0301-2.0850.31861220.241199383
2.085-2.14640.27391320.2312216289
2.1464-2.21560.23751430.2269234097
2.2156-2.29480.21721470.2118239099
2.2948-2.38670.28891460.21652403100
2.3867-2.49530.26641500.20272428100
2.4953-2.62690.23031470.204240599
2.6269-2.79140.2221490.20732445100
2.7914-3.00690.23851470.20952406100
3.0069-3.30950.24141500.1968243599
3.3095-3.78820.25921480.1869243499
3.7882-4.7720.20171510.1598247199
4.772-47.9070.22511560.1882257799
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)
13.6387-1.6042-0.0293.4817-0.83083.01490.09120.3184-0.3972-0.277-0.06150.16230.4155-0.125-0.01770.40650.0121-0.06510.357-0.04870.2912-18.612-12.7314-21.1765
23.1203-1.1819-0.04612.8276-0.62141.9696-0.00150.1154-0.1889-0.0101-0.0528-0.16570.23130.04910.0460.38780.0095-0.04350.2979-0.01350.3146-14.3526-13.7723-11.8187
37.64621.51120.80212.9316-0.86643.48750.0241-0.2744-0.0098-0.32420.07432.27490.8486-1.5086-0.23620.6136-0.1537-0.19930.79010.02061.1067-40.5644-8.0673-18.6598
40.31440.29430.28390.7370.2870.81060.506-0.5893-0.60290.0928-0.73840.93270.19480.2858-0.03380.8859-0.0873-0.06611.27140.21921.4201-42.3737-19.3087-22.8525
55.38990.78861.51083.60890.08617.06140.1571-0.145-0.15250.0402-0.0420.5511-0.0247-0.792-0.08480.34930.05510.01680.3564-0.04370.3666-29.6836-5.2049-11.3366
64.98221.86032.1222.35041.63946.01310.11870.4571-0.0009-0.3596-0.00410.0991-0.0747-0.2113-0.06870.40470.0733-0.05360.33510.03180.2646-21.1598-0.1487-27.7692
72.9839-2.18530.50275.40180.52953.2794-0.0101-0.08520.1707-0.05950.00580.3945-0.2726-0.20030.0040.33780.0339-0.00490.23440.04030.343-26.038227.6744-9.563
87.7783.3797-2.73894.3888-2.56446.72990.22820.828-0.1439-1.3455-0.4101-1.7539-0.12161.77130.12930.6726-0.00810.28620.92410.08850.8451-6.614823.8322-24.513
90.7780.78611.06282.86582.2422.336-0.09620.46630.6241-0.41360.3091-0.08790.5441-0.1401-0.04051.5827-0.3238-0.0781.12710.35111.34-6.615939.6354-30.0144
104.21080.49781.43673.3075-0.85465.4026-0.10280.46680.5014-0.35230.0693-0.4111-0.26521.00160.00160.47550.00630.06860.51680.06230.4985-11.314422.1741-15.1131
115.3126-0.36980.13454.5211-0.15634.83590.00540.86730.3098-0.9805-0.30360.6291-0.5844-0.30620.11050.55260.1146-0.15060.3808-0.0350.4398-28.44316.7809-24.5236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 409 through 454 )A409 - 454
2X-RAY DIFFRACTION2chain 'A' and (resid 455 through 510 )A455 - 510
3X-RAY DIFFRACTION3chain 'A' and (resid 511 through 530 )A511 - 530
4X-RAY DIFFRACTION4chain 'A' and (resid 531 through 557 )A531 - 557
5X-RAY DIFFRACTION5chain 'A' and (resid 558 through 585 )A558 - 585
6X-RAY DIFFRACTION6chain 'A' and (resid 586 through 630 )A586 - 630
7X-RAY DIFFRACTION7chain 'B' and (resid 409 through 510 )B409 - 510
8X-RAY DIFFRACTION8chain 'B' and (resid 511 through 528 )B511 - 528
9X-RAY DIFFRACTION9chain 'B' and (resid 529 through 550 )B529 - 550
10X-RAY DIFFRACTION10chain 'B' and (resid 551 through 585 )B551 - 585
11X-RAY DIFFRACTION11chain 'B' and (resid 586 through 630 )B586 - 630

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