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- PDB-6vte: Naegleria gruberi RNA Ligase K170M mutant with AMP and Mn -

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Basic information

Entry
Database: PDB / ID: 6vte
TitleNaegleria gruberi RNA Ligase K170M mutant with AMP 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 MONOPHOSPHATE / : / Predicted protein
Function and homology information
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / 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: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0663
Polymers38,6641
Non-polymers4022
Water3,495194
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)54.916, 54.916, 102.244
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: 38663.848 Da / Num. of mol.: 1 / Mutation: K170M
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: NgRnlK170M (9.8 mg/ml) was adjusted to 5 mM AMP and 2 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: NgRnlK170M (9.8 mg/ml) was adjusted to 5 mM AMP and 2 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, 30% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 28362 / % possible obs: 86.6 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.068 / Rrim(I) all: 0.116 / Χ2: 3.856 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.141.30.2474830.7790.2340.3411.59546.9
2.14-2.181.40.2315690.8050.2160.3182.00955.6
2.18-2.221.40.2366260.7940.2190.3231.9461.1
2.22-2.261.50.2237240.7440.2050.3042.47374.1
2.26-2.311.60.2178400.8780.1930.2922.25980.7
2.31-2.371.80.1918390.8980.1620.2512.3485.4
2.37-2.422.20.1959740.9060.150.2482.61893.1
2.42-2.492.40.1889660.9150.1420.2362.98496.7
2.49-2.562.40.179680.9410.1260.2132.7496.4
2.56-2.652.40.1649840.9310.1230.2063.45795.6
2.65-2.742.50.1659630.9350.1210.2063.41194.6
2.74-2.852.30.1459250.940.1120.1844.23593.6
2.85-2.982.50.1319750.9650.0940.1624.3196.3
2.98-3.142.50.1369580.9590.0980.1694.77895.3
3.14-3.332.50.1099360.9720.0780.1355.44293.3
3.33-3.592.30.0929420.9730.0670.1155.20792.7
3.59-3.952.60.0859900.9780.0620.1064.8895.5
3.95-4.522.50.0769410.9750.0570.0955.20194.2
4.52-5.692.70.0719700.980.050.0883.97696.3
5.69-302.70.0589700.9250.0420.0723.16994.8

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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: 2.1→27.7 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 2.04 / Phase error: 31.04
RfactorNum. reflection% reflection
Rfree0.2531 2827 9.97 %
Rwork0.189 --
obs0.1955 28362 70.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.79 Å2 / Biso mean: 37.6561 Å2 / Biso min: 14.84 Å2
Refinement stepCycle: final / Resolution: 2.1→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 24 194 2909
Biso mean--33.17 39.41 -
Num. residues----336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.130.3334600.251555361330
2.13-2.170.3357830.265464372636
2.17-2.210.4286840.265474382740
2.21-2.260.3767880.2599925101351
2.26-2.310.3031170.25441076119357
2.31-2.360.35911230.23791112123563
2.36-2.420.27221400.23111389152974
2.42-2.490.32811540.2281466162081
2.49-2.560.33281540.23841461161581
2.56-2.640.2781700.24251509167981
2.64-2.740.35431610.24521456161780
2.74-2.850.2761580.2391306146475
2.85-2.980.31461760.2381527170383
2.98-3.130.30921700.22771477164782
3.13-3.330.29751720.20441402157478
3.33-3.580.22911620.17331380154276
3.59-3.940.21081680.16121550171883
3.94-4.510.2091490.13941472162181
4.51-5.670.19981610.13621559172086
5.68-27.70.15951770.14091529170684
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)
10.52780.01360.07450.7339-0.21790.2967-0.0967-0.0548-0.2501-0.1492-0.0322-0.12140.08990.180.00010.24850.01210.02930.20940.02070.2602-15.0477-31.0426-15.967
20.0217-0.00550.01990.02560.06920.04610.1024-0.05710.2519-0.36210.0854-0.3057-0.29420.0681-0.00050.3426-0.08420.05450.37230.02760.3608-1.75-10.8319-6.6639
30.55220.31160.40470.71640.4140.8196-0.0598-0.03730.09990.04310.01840.08220.00310.000100.18930.0052-0.00170.13740.00480.156-17.6968-2.8855-4.8857
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 137 )A118 - 137
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 339 )A138 - 339

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