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- PDB-6vt4: Naegleria gruberi RNA ligase R149A mutant apo -

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Basic information

Entry
Database: PDB / ID: 6vt4
TitleNaegleria gruberi RNA ligase R149A mutant apo
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 / Predicted protein
Function and homology information
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 / 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: RNA Ligase


Theoretical massNumber of molelcules
Total (without water)38,5761
Polymers38,5761
Non-polymers00
Water1,856103
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)55.244, 55.244, 98.932
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The NgrRnlR149A protein sample (8.2 mg/ml) was mixed with equal volume (1 ul) of 0.1 M HEPES pH 6.5, 30% 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: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 32271 / % possible obs: 99.3 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.034 / Rrim(I) all: 0.053 / Χ2: 1.619 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.1920.359120.780.3010.4631.30499.7
2.19-2.232.20.2838870.850.2450.3761.20799.6
2.23-2.272.40.2319240.8870.1920.3021.2999.8
2.27-2.322.40.2219120.910.1840.2891.16799.8
2.32-2.372.40.1818810.9370.150.2371.20699.8
2.37-2.422.40.1549150.9470.1280.2011.31599.9
2.42-2.482.40.1379010.9580.1140.1791.32799.8
2.48-2.552.40.1249120.9630.1030.1611.499.9
2.55-2.622.40.0969280.980.0790.1251.34199.9
2.62-2.712.40.0818820.9850.0670.1051.34199.8
2.71-2.812.40.0689020.9890.0560.0891.48999.9
2.81-2.922.40.0579350.9920.0470.0741.65999.9
2.92-3.052.40.0469110.9950.0380.061.69499.9
3.05-3.212.40.0388850.9960.0310.051.80399.9
3.21-3.412.40.0359200.9960.0290.0461.94699.9
3.41-3.672.40.0329000.9960.0260.0422.00199.6
3.67-4.042.30.0368970.9960.030.0462.64299
4.04-4.632.30.0328810.9960.0270.0422.7796.9
4.63-5.822.30.0328940.9960.0270.0422.42899.6
5.82-302.30.0218640.9980.0170.0271.08493.9

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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: 2.16→27.15 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.56
RfactorNum. reflection% reflection
Rfree0.2517 3229 10.01 %
Rwork0.1887 --
obs0.1949 32271 88.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.73 Å2 / Biso mean: 51.0313 Å2 / Biso min: 23.47 Å2
Refinement stepCycle: final / Resolution: 2.16→27.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 0 103 2796
Biso mean---48.67 -
Num. residues----337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.190.30591100.27891066117675
2.19-2.220.36951330.26411176130980
2.22-2.260.27321250.24871153127883
2.26-2.30.31011470.25121256140387
2.3-2.340.30491340.24741213134787
2.34-2.390.29491650.241270143588
2.39-2.430.31461380.24121214135288
2.44-2.490.31141380.241231136988
2.49-2.550.31231300.25591236136688
2.55-2.610.30441470.2431296144389
2.61-2.680.3211380.24761259139789
2.68-2.760.33451480.22641343149190
2.76-2.850.34021230.22561241136490
2.85-2.950.27721340.23841266140091
2.95-3.070.29331460.22321354150092
3.07-3.210.27621420.23851291143391
3.21-3.370.28061580.20851291144993
3.38-3.590.27771450.18211291143692
3.59-3.860.24561480.17031333148193
3.87-4.250.19491430.1571356149993
4.25-4.860.18921490.12871275142492
4.86-6.110.20551480.14471357150594
6.13-27.150.17211400.13681274141490
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)
11.3401-0.1585-0.4862.2719-0.2521.1654-0.2231-0.2241-0.2962-0.2326-0.0974-0.51590.1810.1903-0.00060.3737-0.01990.09830.28510.05750.4607-14.7105-30.8656-14.5594
20.14320.1750.36280.77730.32530.9535-0.140.1714-0.12120.11670.134-0.14210.04320.0152-0.00060.3485-0.02920.00340.2888-0.01430.2574-17.3517-10.5289-4.1636
30.79510.85960.54451.81370.79951.4703-0.22120.0390.1835-0.08540.12550.1301-0.10040.0659-0.00020.3073-0.00240.0050.22880.00310.2611-16.9468-1.0456-4.7662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 122 )A3 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 173 )A123 - 173
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 339 )A174 - 339

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