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- PDB-6vtb: Naegleria gruberi RNA ligase K326A mutant with ATP and Mn -

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Basic information

Entry
Database: PDB / ID: 6vtb
TitleNaegleria gruberi RNA ligase K326A 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: 1.547 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.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)39,2765
Polymers38,6041
Non-polymers6724
Water12,665703
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)53.031, 64.221, 101.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA ligase


Mass: 38603.730 Da / Num. of mol.: 1 / Mutation: K326A
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.: 703 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: NgrRnlK326A (21.4 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: NgrRnlK326A (21.4 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, 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: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.547→50 Å / Num. obs: 94052 / % possible obs: 96.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.035 / Rrim(I) all: 0.112 / Χ2: 2.139 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.547-1.588.10.91423700.7920.3320.9751.56493.8
1.58-1.618.50.80224140.7710.2860.8541.5995
1.61-1.648.90.66624210.8710.230.7061.63296.2
1.64-1.679.90.58724220.8910.1930.6191.67195.2
1.67-1.7110.10.5124310.9190.1640.5361.64895.8
1.71-1.7510.10.42824250.9440.1380.451.67596.1
1.75-1.79100.33924330.9650.1090.3561.75896.2
1.79-1.84100.27824880.9770.090.2931.84497
1.84-1.899.80.26925110.9820.0880.2831.94397.8
1.89-1.959.80.18824860.9850.0620.1982.24198.5
1.95-2.029.80.16125360.9910.0530.172.03698.9
2.02-2.19.70.12625170.9930.0410.1332.198.9
2.1-2.29.60.11425620.9930.0380.122.17398.8
2.2-2.329.30.10525350.9950.0350.1112.55698.8
2.32-2.469.70.08525280.9960.0280.092.20199.1
2.46-2.659.60.08225690.9960.0270.0862.43199.3
2.65-2.929.70.07325990.9970.0240.0772.91699.8
2.92-3.349.80.06526160.9980.0220.0683.427100
3.34-4.218.30.05122310.9980.0180.0543.04884.3
4.21-5010.30.03927780.9990.0130.0422.299.2

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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: 1.547→28.6 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.01
RfactorNum. reflection% reflection
Rfree0.1947 3770 4.01 %
Rwork0.1632 --
obs0.1644 94052 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.41 Å2 / Biso mean: 17.7892 Å2 / Biso min: 3.89 Å2
Refinement stepCycle: final / Resolution: 1.547→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 34 703 3450
Biso mean--9.74 28.95 -
Num. residues----340
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.547-1.56640.27481210.259292983
1.5664-1.5870.26961370.2387329296
1.587-1.60870.27611390.2269330994
1.6087-1.63170.23561410.2139333297
1.6317-1.65610.26851390.2007335494
1.6561-1.68190.27021390.1955331396
1.6819-1.70950.20731370.1886334295
1.7095-1.7390.1691380.1855334796
1.739-1.77060.231390.1838338296
1.7706-1.80460.2271360.1674330897
1.8046-1.84150.21231380.181334496
1.8415-1.88150.19021460.1867342297
1.8815-1.92530.23191400.1917333897
1.9253-1.97340.21781500.1658343697
1.9734-2.02680.19181460.1665338698
2.0268-2.08640.23411450.1626340398
2.0864-2.15370.16041420.1526341098
2.1537-2.23060.18791400.1634341298
2.2306-2.31990.18661440.1751340397
2.3199-2.42540.1951370.1579340898
2.4254-2.55320.19651410.1632342498
2.5532-2.71310.19091440.1596341999
2.7131-2.92240.18921470.15363516100
2.9224-3.21610.19221480.14983480100
3.2161-3.68070.16261320.1335320992
3.6807-4.63410.13951180.1282289482
4.6341-28.60.18081460.14163470100
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)
10.2397-0.0124-0.10270.21650.04530.22550.0017-0.0364-0.0090.0282-0.02290.01670.0042-0.0591-0.01930.0579-0.0011-0.00410.0754-0.00290.06940.15867.4552122.9908
20.49370.0672-0.24690.24640.0570.4155-0.00220.0620.0012-0.02580.0292-0.0116-0.024-0.05390.00010.0473-0.0075-0.00070.0428-0.0010.040564.172264.469107.2033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 119 )A0 - 119
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 339 )A120 - 339

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