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- PDB-6vtf: Naegleria gruberi RNA ligase with PPi -

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Basic information

Entry
Database: PDB / ID: 6vtf
TitleNaegleria gruberi RNA ligase with PPi
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 / PYROPHOSPHATE 2- / Predicted protein
Function and homology information
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,3518
Polymers154,6474
Non-polymers7044
Water2,090116
1
A: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8382
Polymers38,6621
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8382
Polymers38,6621
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8382
Polymers38,6621
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8382
Polymers38,6621
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.745, 104.896, 120.073
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: VAL / Beg label comp-ID: VAL / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 3 - 339 / Label seq-ID: 4 - 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: 38661.832 Da / Num. of mol.: 4
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-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: NgRnl wild type (10 mg/ml) was adjusted to 1 mM PPi 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 ...Details: NgRnl wild type (10 mg/ml) was adjusted to 1 mM PPi 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: 2.7→30.21 Å / Num. obs: 41889 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.049 / Rrim(I) all: 0.101 / Χ2: 1.098 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.60.41920440.7560.2510.4910.83597.3
2.75-2.83.40.37620330.8060.2250.4410.86596.8
2.8-2.853.90.3420870.8560.1890.3910.86197.4
2.85-2.9140.29821050.8880.1650.3420.90698.7
2.91-2.9740.26320720.9070.1470.3030.96398.7
2.97-3.043.90.23321110.9240.1310.2691.0298.9
3.04-3.123.90.19820880.9490.1110.2281.03998.3
3.12-3.23.90.18420940.9520.1030.2121.06698.5
3.2-3.293.90.15520900.9610.0880.1791.15498.2
3.29-3.43.60.13620580.9740.080.1591.25497.4
3.4-3.523.90.12220940.9790.0680.141.25197.2
3.52-3.664.20.11520820.9810.0620.1311.32397.8
3.66-3.834.10.10720920.9840.0580.1221.33398.1
3.83-4.034.10.09521170.9870.0520.1081.35597.8
4.03-4.2840.08120930.9920.0440.0931.28297.1
4.28-4.613.80.06920670.9930.0390.0791.26495.7
4.61-5.074.20.06821240.9920.0360.0781.198.2
5.07-5.84.20.06421110.9940.0340.0720.99996.6
5.8-7.33.90.05721100.9950.0320.0660.92595.2
7.3-3040.04422170.9980.0240.051.07194.9

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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: 2.71→30.21 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.45
RfactorNum. reflection% reflection
Rfree0.274 1974 4.72 %
Rwork0.2176 --
obs0.2202 41850 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.74 Å2 / Biso mean: 63.2337 Å2 / Biso min: 18.08 Å2
Refinement stepCycle: final / Resolution: 2.71→30.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10796 0 36 116 10948
Biso mean--96.61 51.4 -
Num. residues----1348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4124X-RAY DIFFRACTION7.938TORSIONAL
12B4124X-RAY DIFFRACTION7.938TORSIONAL
13C4124X-RAY DIFFRACTION7.938TORSIONAL
14D4124X-RAY DIFFRACTION7.938TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.71-2.780.38531110.29852292240379
2.78-2.850.37691430.29452842298597
2.85-2.930.37991340.29162874300899
2.93-3.030.34641530.28262881303499
3.03-3.140.33061410.27162876301798
3.14-3.260.35031440.2512926307099
3.26-3.410.30071450.24622840298598
3.41-3.590.26881440.22792863300798
3.59-3.820.26951440.21852891303598
3.82-4.110.25311390.20192909304898
4.11-4.520.23111370.16662880301796
4.52-5.170.20871400.16662913305398
5.17-6.50.2341490.20782911306097
6.51-30.210.2731500.20992978312894
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)
13.0429-0.5853-1.7893.65110.61514.13420.0195-0.15570.13990.24510.0290.10610.2734-0.01290.0350.27840.013-0.01190.435-0.00480.4752-44.36961.9712-8.194
20.6706-0.0529-1.11152.792-1.80037.06770.1313-0.04960.1103-0.0924-0.0597-0.36630.19080.4422-0.09610.43170.0712-0.02670.4865-0.05010.4993-37.63174.942-37.1836
32.8242-0.78480.74943.60920.38553.00760.06370.2323-0.2337-0.0007-0.11240.0216-0.0259-0.01150.02280.2479-0.00770.02640.26740.00630.2745-46.207349.3121-54.1497
41.17850.86590.25930.6655-0.80753.48540.1134-0.061-0.07530.42-0.22650.0069-0.4993-0.04350.03590.56550.0420.05080.4212-0.01150.2784-43.251446.1037-31.8581
52.6373-0.53660.86193.4241-0.69223.46140.1802-0.0251-0.20.3474-0.1836-0.2407-0.59350.2988-0.02980.6316-0.05990.01770.45840.08220.2508-36.660842.2144-18.6514
64.50881.47930.16422.3906-0.72743.8238-0.2886-0.0853-0.1640.4912-0.0951-0.1176-0.99690.45080.21090.7673-0.02050.00090.37480.05250.293-39.797958.2558-32.9481
71.9881-1.67341.3561.9147-0.15133.7621-0.36140.13430.13930.54820.16210.3738-0.23770.05620.10920.4532-0.03210.19060.38270.04510.2718-42.898529.7229-76.5445
82.6838-0.01331.13412.4908-0.90951.3881-0.10740.0023-0.4312-0.38630.0669-0.21720.48030.37980.06070.5124-0.02180.1330.3194-0.03560.2734-44.914417.7514-72.8437
96.71163.6628-0.12052.54520.31181.41070.147-0.3136-0.52820.0659-0.1382-0.1415-0.0557-0.10250.020.23180.02990.04170.32250.02460.4361-73.515517.9207-65.6054
105.81040.9672-0.15062.54020.20093.9136-0.0933-0.47310.91820.12-0.1802-0.07-0.2207-0.23820.10790.3872-0.11210.04180.2803-0.0390.3818-62.048931.5667-66.1532
112.94710.4353-0.06123.53810.26183.1590.1005-0.223-0.10650.2227-0.2462-0.1708-0.44020.77320.14450.3953-0.0837-0.02640.47390.09960.276-41.24929.339613.1452
124.212-1.0710.85372.87980.08151.8165-0.03050.03290.4579-0.0956-0.24080.533-0.1203-0.14150.24390.2812-0.04210.00040.4133-0.10870.648-69.494731.73635.3304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 119 )A3 - 119
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 339 )A120 - 339
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 119 )B3 - 119
4X-RAY DIFFRACTION4chain 'B' and (resid 120 through 173 )B120 - 173
5X-RAY DIFFRACTION5chain 'B' and (resid 174 through 284 )B174 - 284
6X-RAY DIFFRACTION6chain 'B' and (resid 285 through 339 )B285 - 339
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 29 )C3 - 29
8X-RAY DIFFRACTION8chain 'C' and (resid 30 through 137 )C30 - 137
9X-RAY DIFFRACTION9chain 'C' and (resid 138 through 284 )C138 - 284
10X-RAY DIFFRACTION10chain 'C' and (resid 285 through 339 )C285 - 339
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 119 )D3 - 119
12X-RAY DIFFRACTION12chain 'D' and (resid 120 through 339 )D120 - 339

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