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- PDB-6lhx: Crystal structure of ThsA -

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Basic information

Entry
Database: PDB / ID: 6lhx
TitleCrystal structure of ThsA
ComponentsThsA
KeywordsHYDROLASE / NAD+ hydrolysis
Function / homology
Function and homology information


NAD+ glycohydrolase / defense response to virus / hydrolase activity / nucleotide binding / cytoplasm
Similarity search - Function
NAD(+) hydrolase ThsA, Sir2/TIR-associating SLOG domain / Sir2- and TIR-associating SLOG family / SIR2-like domain / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
NAD(+) hydrolase ThsA
Similarity search - Component
Biological speciesBacillus cereus MSX-D12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.501 Å
AuthorsBae, E. / Ka, D. / Oh, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1086298 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2020
Title: Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD+degradation.
Authors: Ka, D. / Oh, H. / Park, E. / Kim, J.H. / Bae, E.
History
DepositionDec 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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: ThsA
B: ThsA
C: ThsA
D: ThsA


Theoretical massNumber of molelcules
Total (without water)222,2784
Polymers222,2784
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.424, 168.584, 93.614
Angle α, β, γ (deg.)90.000, 106.710, 90.000
Int Tables number5
Space group name H-MC121
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: HIS / Beg label comp-ID: HIS

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNchain AAA2 - 4762 - 476
2ASNASNchain BBB2 - 4762 - 476
3SERSERchain CCC2 - 4752 - 475
4SERSERchain DDD2 - 4752 - 475

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Components

#1: Protein
ThsA


Mass: 55569.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Bacillus cereus MSX-D12 (bacteria) / Gene: II9_05448 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J8G6Z1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22% PPG400, 0.1 M MES pH 6.5, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 181015 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 63.54 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.055 / Net I/σ(I): 10.54
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 1.666 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 9063 / CC1/2: 0.543 / Rpim(I) all: 0.665 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
AutoSolphasing
PDB_EXTRACT3.25data extraction
PHENIXmodel building
BUCCANEERmodel building
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.501→31.641 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 3958 2.19 %
Rwork0.2417 177057 -
obs0.2424 181015 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 329.3 Å2 / Biso mean: 82.1693 Å2 / Biso min: 32.32 Å2
Refinement stepCycle: final / Resolution: 2.501→31.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13296 0 0 36 13332
Biso mean---55.14 -
Num. residues----1726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313534
X-RAY DIFFRACTIONf_angle_d0.8118340
X-RAY DIFFRACTIONf_chiral_restr0.0322093
X-RAY DIFFRACTIONf_plane_restr0.0042364
X-RAY DIFFRACTIONf_dihedral_angle_d13.1634762
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7397X-RAY DIFFRACTION9.89TORSIONAL
12B7397X-RAY DIFFRACTION9.89TORSIONAL
13C7397X-RAY DIFFRACTION9.89TORSIONAL
14D7397X-RAY DIFFRACTION9.89TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5012-2.53170.3491370.341604994
2.5317-2.56380.39541370.3369621198
2.5638-2.59750.38351420.3313627098
2.5975-2.6330.3741400.3347627099
2.633-2.67060.39551400.3337626299
2.6706-2.71050.35591390.3344630599
2.7105-2.75280.38041430.3227638499
2.7528-2.79790.37191380.3212626399
2.7979-2.84610.36431390.3158628399
2.8461-2.89790.31791400.2986628599
2.8979-2.95360.32471460.297637899
2.9536-3.01380.34171420.2971636999
3.0138-3.07930.36651380.293626199
3.0793-3.15080.32021460.2798638299
3.1508-3.22960.30411400.28066352100
3.2296-3.31680.32861400.27236343100
3.3168-3.41430.30331400.24896322100
3.4143-3.52440.28021430.24626385100
3.5244-3.65010.29351450.23236346100
3.6501-3.79610.24161400.23266337100
3.7961-3.96850.21361440.22336426100
3.9685-4.17730.27381410.21166344100
4.1773-4.43840.24891430.20686402100
4.4384-4.780.19111420.19186359100
4.78-5.2590.23361440.20236358100
5.259-6.01550.27541430.23346398100
6.0155-7.56180.31281430.24636359100
7.5618-31.6410.19231430.2067635499
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)
11.43121.12421.54813.95721.22671.9229-0.16740.41120.1353-0.32720.0251-0.0068-0.0533-0.10820.18810.46510.01380.13080.57110.04440.3902-24.718523.4043-9.747
22.95060.0357-1.19781.41980.41023.2418-0.34690.5389-0.2785-0.01890.01540.140.6905-0.51140.29850.6453-0.14050.10820.4967-0.0610.417-33.73429.176-6.5766
33.90190.26351.51475.81911.58426.7264-0.31190.9457-0.1022-0.7686-0.10210.35210.3807-0.5980.41480.6385-0.15630.17970.8792-0.07810.5212-58.535712.01815.6255
44.20311.97592.0266.73741.00673.61150.092-0.5647-0.75210.3516-0.0894-0.24080.8041-0.1563-0.0330.6041-0.04130.20950.59160.14940.5255-17.39653.194817.638
55.55090.00811.18320.71170.0050.0825-0.0588-0.4684-0.07370.04850.0553-0.082-0.04470.10680.05030.55310.01070.15110.63080.08170.409-6.57912.30420.4203
63.0281-2.4509-0.12951.9690.11720.07740.0327-1.07551.41761.03130.11910.4662-0.5616-0.38360.07010.72510.00890.16580.9481-0.37210.9093-49.249731.202231.9122
74.28680.34280.41963.07640.06534.33820.0397-1.11050.28370.3701-0.1336-0.07060.38860.27630.14250.6477-0.040.2251.069-0.14220.4953-42.440920.228633.1403
82.1831-0.51550.55992.8813-0.64542.2099-0.0954-0.50490.16020.34730.10450.1564-0.0832-0.2135-0.04030.46670.03620.16220.4883-0.02320.4383-22.327846.60759.1666
92.4047-0.05840.81861.02950.59722.6881-0.3305-1.05810.18020.140.08960.2108-0.5193-0.95750.1450.69310.22950.20670.7381-0.15140.7607-40.364560.02189.1455
106.23410.0978-0.54453.43590.41286.5183-0.1012-0.4951-0.73960.3452-0.25480.6221-0.1856-0.98470.38190.62260.16560.10160.7452-0.13410.8401-57.583556.4872-9.0575
115.5722-0.8343-0.86882.29060.33343.56230.02450.80381.1049-0.5087-0.05790.0912-0.83490.06870.07970.56190.01310.01530.4160.23280.6074-15.521563.2245-17.0253
126.1134-0.4429-0.54991.08880.66141.7341-0.04741.09730.3007-0.3669-0.1278-0.1235-0.3470.47330.05750.65920.03590.08710.660.15350.5238-5.869654.0664-23.4411
135.175-0.1779-2.57824.15441.09245.9963-0.04481.5558-0.9971-0.6067-0.37090.1961-0.0035-0.70170.37710.69130.16390.03271.0305-0.35270.8231-42.486348.1688-35.1842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 164 )A2 - 164
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 340 )A165 - 340
3X-RAY DIFFRACTION3chain 'A' and (resid 341 through 476 )A341 - 476
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 176 )B2 - 176
5X-RAY DIFFRACTION5chain 'B' and (resid 177 through 288 )B177 - 288
6X-RAY DIFFRACTION6chain 'B' and (resid 289 through 315 )B289 - 315
7X-RAY DIFFRACTION7chain 'B' and (resid 316 through 476 )B316 - 476
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 220 )C2 - 220
9X-RAY DIFFRACTION9chain 'C' and (resid 221 through 315 )C221 - 315
10X-RAY DIFFRACTION10chain 'C' and (resid 316 through 475 )C316 - 475
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 202 )D2 - 202
12X-RAY DIFFRACTION12chain 'D' and (resid 203 through 290 )D203 - 290
13X-RAY DIFFRACTION13chain 'D' and (resid 291 through 475 )D291 - 475

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