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- PDB-6vt8: Naegleria gruberi RNA ligase E312A mutant with AMP and Mn -

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Basic information

Entry
Database: PDB / ID: 6vt8
TitleNaegleria gruberi RNA ligase E312A 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: 1.998 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)39,0063
Polymers38,6041
Non-polymers4022
Water4,810267
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)54.941, 54.941, 100.602
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: 38603.797 Da / Num. of mol.: 1 / Mutation: E312A
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.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: NgrRnlE312A (9.1 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: NgrRnlE312A (9.1 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, 25% 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: 1.998→30 Å / Num. obs: 42536 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.046 / Rrim(I) all: 0.088 / Χ2: 2.915 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.998-2.033.40.5811950.6480.3660.6881.77100
2.03-2.073.40.52911190.7530.3370.631.85499.8
2.07-2.113.50.40411620.8360.2530.4781.877100
2.11-2.153.40.35611360.8420.2270.4241.994100
2.15-2.23.40.30911830.8780.1940.3662.16499.9
2.2-2.253.40.26911130.9090.170.322.239100
2.25-2.313.40.23811650.9330.1480.2812.235100
2.31-2.373.40.22711460.940.1420.2692.48899.7
2.37-2.443.50.20311620.9520.1260.2392.574100
2.44-2.523.40.17811560.9620.110.212.793100
2.52-2.613.50.14811490.9720.0910.1742.729100
2.61-2.713.50.13111670.9770.080.1543.00999.9
2.71-2.843.50.10411000.9830.0630.1223.24599.8
2.84-2.993.50.08411880.9920.0510.0993.52299.7
2.99-3.173.50.07511290.9910.0450.0884.16399.3
3.17-3.423.40.06111490.9940.0370.0724.59799.1
3.42-3.763.40.05411270.9940.0330.0635.06998.6
3.76-4.313.40.04611430.9950.0290.0554.35698.8
4.31-5.423.50.03811450.9980.0230.0453.38499.3
5.42-303.80.02911380.9990.0170.0342.38798

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5COT

5cot


Resolution: 1.998→27.41 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.2333 3695 8.69 %
Rwork0.1872 --
obs0.1912 42536 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.18 Å2 / Biso mean: 33.2211 Å2 / Biso min: 16.56 Å2
Refinement stepCycle: final / Resolution: 1.998→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 23 267 2978
Biso mean--23.09 36.77 -
Num. residues----336
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.998-2.02390.38651450.3121146188
2.0239-2.05160.32111620.3187147291
2.0516-2.08090.3321320.2907148291
2.0809-2.1120.33651550.2626148792
2.112-2.1450.3251220.2739140891
2.145-2.18010.29371390.2716154492
2.1801-2.21770.28571550.2586149692
2.2177-2.2580.32071430.2459148492
2.258-2.30140.27521100.2242153592
2.3014-2.34840.26421390.2312145792
2.3484-2.39940.25181640.2202150993
2.3994-2.45520.2861360.2221147592
2.4552-2.51650.29751610.2276148693
2.5165-2.58450.27061280.2205150693
2.5845-2.66050.3161460.2143149693
2.6605-2.74630.25051400.2135154593
2.7463-2.84440.2791390.2022146893
2.8444-2.95810.29651440.202151793
2.9581-3.09260.2141360.1915154293
3.0926-3.25540.23251510.1836145192
3.2554-3.4590.18461480.1697150591
3.459-3.72540.18661260.1514143390
3.7254-4.09920.20081470.1452147491
4.0992-4.68980.16151350.1304147993
4.6898-5.8990.19891400.1479155796
5.899-27.410.16441520.1416157296

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