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- PDB-6vtg: Naegleria gruberi RNA ligase E227A mutant apo -

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Basic information

Entry
Database: PDB / ID: 6vtg
TitleNaegleria gruberi RNA ligase E227A 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 / Predicted protein
Function and homology information
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA ligase
B: RNA ligase
C: RNA ligase
D: RNA ligase


Theoretical massNumber of molelcules
Total (without water)154,4154
Polymers154,4154
Non-polymers00
Water1,65792
1
A: RNA ligase


Theoretical massNumber of molelcules
Total (without water)38,6041
Polymers38,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA ligase


Theoretical massNumber of molelcules
Total (without water)38,6041
Polymers38,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA ligase


Theoretical massNumber of molelcules
Total (without water)38,6041
Polymers38,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA ligase


Theoretical massNumber of molelcules
Total (without water)38,6041
Polymers38,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.101, 104.037, 119.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 0 - 339 / Label seq-ID: 1 - 340

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
RNA ligase /


Mass: 38603.797 Da / Num. of mol.: 4 / Mutation: E227A
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 / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The NgrRnlE227A protein sample (12 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-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→30 Å / Num. obs: 102490 / % possible obs: 99.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.053 / Rrim(I) all: 0.124 / Χ2: 2.371 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.49-2.545.50.81327090.6680.3760.8980.85599.8
2.54-2.595.30.726920.7370.3270.7760.90599.9
2.59-2.646.10.62426790.80.2740.6830.9299.9
2.64-2.696.10.55627030.8350.2440.6090.993100
2.69-2.756.10.46526850.8540.2030.5081.1999.7
2.75-2.8260.41527270.8730.1830.4541.297100
2.82-2.8960.36527130.8840.1620.41.52599.9
2.89-2.965.90.30526800.9280.1370.3361.68799.7
2.96-3.055.70.26727160.9260.1230.2951.98199.9
3.05-3.155.20.22827120.9450.110.2542.12799.2
3.15-3.265.80.19627090.960.090.2172.31499.7
3.26-3.395.90.16326980.9740.0740.1792.55399.9
3.39-3.555.80.14227320.9770.0660.1582.94999.7
3.55-3.735.70.12627020.9730.0590.1393.17899.3
3.73-3.975.50.11327310.9810.0540.1263.46799.3
3.97-4.275.10.10227000.9740.0510.1154.35198.1
4.27-4.75.50.09227320.9810.0440.1024.58898.8
4.7-5.385.30.09227350.9860.0450.1035.18398.7
5.38-6.765.20.07727550.9840.0380.0864.1397.5
6.76-305.50.04928700.9970.0230.0542.16897.3

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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: 2.49→29.73 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31
RfactorNum. reflection% reflection
Rfree0.2732 3777 3.71 %
Rwork0.215 --
obs0.2172 102490 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.11 Å2 / Biso mean: 82.0559 Å2 / Biso min: 25.8 Å2
Refinement stepCycle: final / Resolution: 2.49→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10852 0 0 92 10944
Biso mean---55.89 -
Num. residues----1360
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4148X-RAY DIFFRACTION10.833TORSIONAL
12B4148X-RAY DIFFRACTION10.833TORSIONAL
13C4148X-RAY DIFFRACTION10.833TORSIONAL
14D4148X-RAY DIFFRACTION10.833TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.520.34011150.30513367348290
2.52-2.560.36261460.30813667381398
2.56-2.590.40061470.31433640378798
2.59-2.630.3561250.299337273852100
2.63-2.670.30341630.288837573920100
2.67-2.710.33771390.283736833822100
2.71-2.750.30361410.264137933934100
2.75-2.80.42061590.279236903849100
2.8-2.850.32681310.275437333864100
2.85-2.910.3281450.264737303875100
2.91-2.970.32381460.24893733387999
2.97-3.030.28771420.25473699384199
3.03-3.10.32071420.25393749389199
3.1-3.180.3211450.23463593373896
3.18-3.260.32411410.24453672381399
3.26-3.360.30341200.23643746386699
3.36-3.470.31971560.22343683383999
3.47-3.590.33631280.23083676380498
3.59-3.740.30661460.2343604375097
3.74-3.910.27681430.22343633377697
3.91-4.110.25141300.19893554368495
4.11-4.370.22081470.17233562370995
4.37-4.70.19651450.16443585373096
4.7-5.170.22691340.183648378296
5.17-5.920.28111360.20063603373996
5.92-7.440.23431480.20593567371596
7.44-29.730.2121420.16663594373696
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)
14.48480.3235-1.53726.64951.33054.9463-0.0086-0.2120.3888-0.08450.38090.81410.3169-0.4751-0.27350.6213-0.0195-0.04810.82150.11840.7281-42.58061.2739-8.0345
2-0.0161-0.20680.02212.1358-1.29713.9789-0.19660.04690.0477-0.61450.37910.80040.5209-1.0273-0.13530.7664-0.174-0.20850.86250.14080.843-45.16737.074-25.3281
31.1039-1.45640.95532.735-2.51266.06160.3489-0.2761-0.1637-0.383-0.00890.08661.5557-0.5193-0.23860.7928-0.1271-0.11240.5157-0.0070.5099-36.20565.3431-39.3419
44.1375-1.50110.11235.46460.53111.6784-0.01730.151-0.08120.09360.00540.1894-0.0617-0.0433-0.00090.2498-0.00270.03540.35260.02290.3509-46.100749.2012-53.6985
51.06120.28561.79211.8311-1.09165.38310.1366-0.5032-0.04820.5377-0.1531-0.0577-0.16-0.63680.0190.655-0.08650.00550.59660.04570.4255-38.813747.0253-25.4331
61.81760.65820.59765.8257-0.29085.1714-0.05640.0998-0.189-0.3485-0.0073-0.26340.66350.00620.05840.3954-0.04920.08630.3899-0.03050.3463-42.549822.1098-75.2942
75.88121.359-0.44881.8339-0.11610.87150.0462-0.4565-0.25370.0922-0.0563-0.1019-0.03050.14650.03120.3221-0.03270.01740.4414-0.01270.4107-69.54420.6881-65.5919
83.17271.0368-0.03646.08310.46145.3649-0.18420.078-0.23680.0101-0.1186-0.0368-0.00670.35310.2720.6379-0.00090.10510.56370.03130.4665-40.84228.163711.6232
93.6003-0.37261.78071.15430.27961.434-0.22490.09360.2227-0.2198-0.18450.6852-0.2336-0.31870.34560.8215-0.0711-0.0030.784-0.14730.9137-67.130631.8836.582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 100 )A0 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 173 )A101 - 173
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 339 )A174 - 339
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 119 )B0 - 119
5X-RAY DIFFRACTION5chain 'B' and (resid 120 through 339 )B120 - 339
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 119 )C0 - 119
7X-RAY DIFFRACTION7chain 'C' and (resid 120 through 339 )C120 - 339
8X-RAY DIFFRACTION8chain 'D' and (resid 0 through 100 )D0 - 100
9X-RAY DIFFRACTION9chain 'D' and (resid 101 through 339 )D101 - 339

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