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- PDB-6vtd: Naegleria gruberi RNA ligase R149A mutant with ATP and Mn -

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Basic information

Entry
Database: PDB / ID: 6vtd
TitleNaegleria gruberi RNA ligase R149A mutant with ATP and Mn
ComponentsRNA Ligase
KeywordsLIGASE / RNA repair / adenylyltransferase
Function / homologyRNA ligase, DRB0094 / PHA02142 OB-fold domain / RNA ligase domain, REL/Rln2 / RNA ligase / ATP binding / metal ion binding / ADENOSINE-5'-TRIPHOSPHATE / : / Predicted protein
Function and homology information
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUnciuleac, M.C. / Goldgur, Y. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Authors: Unciuleac, M.C. / Goldgur, Y. / Shuman, S.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2485
Polymers38,5761
Non-polymers6724
Water90150
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)88.775, 88.775, 100.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RNA Ligase


Mass: 38575.719 Da / Num. of mol.: 1 / Mutation: R149A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_82186 / Production host: Escherichia coli (E. coli) / References: UniProt: D2W2Z5
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: NgrRnlR149A (8.2 mg/ml) was adjusted to 2 mM ATP and 5 mM MnCl2 and incubated for 15 min on ice before aliquots of the protein solution (1 ul) were mixed on a coverslip with an equal volume ...Details: NgrRnlR149A (8.2 mg/ml) was adjusted to 2 mM ATP and 5 mM MnCl2 and incubated for 15 min on ice before aliquots of the protein solution (1 ul) were mixed on a coverslip with an equal volume of precipitant solution containing 0.1 M HEPES pH 6.5, 27% PEG6000

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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: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 29868 / % possible obs: 99.1 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Χ2: 1.799 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.446.80.87820.7520.3240.8671.397100
2.44-2.497.30.738010.7950.2870.7861.44599.8
2.49-2.537.30.6797880.8210.2670.7311.41699.7
2.53-2.597.20.5277910.8860.2080.5681.41299.7
2.59-2.647.20.4578110.9280.1790.4931.401100
2.64-2.77.30.3857750.9140.150.4141.50299.7
2.7-2.777.30.3028060.9550.1180.3251.49799.8
2.77-2.857.20.237980.9740.0910.2471.47599.5
2.85-2.937.20.1988090.9830.0780.2141.58699.5
2.93-3.027.20.1367900.9920.0530.1471.62599.5
3.02-3.137.20.1098100.9940.0430.1181.68999.5
3.13-3.267.20.0958030.9940.0370.1021.81599
3.26-3.47.20.0728110.9970.0280.0771.73399.5
3.4-3.587.10.0598140.9980.0230.0631.8499.5
3.58-3.817.10.0578030.9980.0230.0622.14999
3.81-4.170.0528130.9980.0210.0562.28598.8
4.1-4.516.90.0518230.9970.0210.0552.76298.8
4.51-5.166.60.0528280.9980.0220.0573.03998.2
5.16-6.496.70.058330.9970.020.0542.44298.1
6.49-306.50.0328850.9990.0130.0351.59394.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5COT

5cot


Resolution: 2.4→27.05 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.64
RfactorNum. reflection% reflection
Rfree0.3063 2977 9.97 %
Rwork0.2463 --
obs0.2521 29868 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 223.16 Å2 / Biso mean: 72.2875 Å2 / Biso min: 32.01 Å2
Refinement stepCycle: final / Resolution: 2.4→27.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 34 50 2770
Biso mean--69.56 56.63 -
Num. residues----336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.440.40411440.365212731417100
2.44-2.480.43391370.359712831420100
2.48-2.530.38231430.356113001443100
2.53-2.580.41711410.341212681409100
2.58-2.630.43041460.351512811427100
2.63-2.690.32481460.328613161462100
2.69-2.750.381410.350712741415100
2.75-2.820.31021400.322312611401100
2.82-2.890.42851430.304112831426100
2.89-2.980.28061440.299313111455100
2.98-3.080.37631380.306812711409100
3.08-3.190.34691460.292512791425100
3.19-3.310.33141440.301712821426100
3.31-3.460.33881430.277512651408100
3.46-3.650.31061410.24731296143799
3.65-3.870.28891430.248912821425100
3.87-4.170.29741410.22512801421100
4.17-4.590.25711420.18921279142199
4.59-5.250.24131420.18681277141999
5.26-6.60.31781430.19961263140699
6.6-27.050.2441290.17971267139697
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)
16.79050.38220.04783.9838-0.96456.0216-0.1652-0.1850.0465-0.20170.34690.44890.3058-0.8724-0.11280.3539-0.0896-0.0720.40230.06110.4382-2.466728.011624.2411
24.0379-2.1158-0.68023.13291.66511.30360.27360.6943-0.2237-0.4089-0.2694-0.32230.49920.12680.01270.76410.15920.0020.5418-0.0060.556718.48113.241215.1702
32.8872-1.3803-0.12454.42312.91891.61040.10650.2095-0.1716-0.13060.2318-0.55610.54430.4263-0.31320.710.2483-0.04020.54230.01980.477825.752913.175123.0832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 117 )A4 - 117
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 200 )A118 - 200
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 339 )A201 - 339

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