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- PDB-8a8g: ATP sulfurylase from Methanothermococcus thermolithotrophicus - o... -

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Basic information

Entry
Database: PDB / ID: 8a8g
TitleATP sulfurylase from Methanothermococcus thermolithotrophicus - orthorhombic form
ComponentsATP sulfurylase from Methanothermococcus thermolithotrophicus
KeywordsTRANSFERASE / sulfate assimilation / methanogens / archaea / APS / ATP / thermophile / methane / activation / marine
Function / homologySulfate adenylyltransferase / Sulfate adenylyltransferase / HUPs / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsJespersen, M. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)WA 4053/1-1 Germany
CitationJournal: Nat Microbiol / Year: 2023
Title: Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus.
Authors: Jespersen, M. / Wagner, T.
History
DepositionJun 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP sulfurylase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,52210
Polymers44,7201
Non-polymers8029
Water3,747208
1
A: ATP sulfurylase from Methanothermococcus thermolithotrophicus
hetero molecules

A: ATP sulfurylase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,04420
Polymers89,4402
Non-polymers1,60418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_857-x+3,y,-z+21
Unit cell
Length a, b, c (Å)55.705, 154.457, 157.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

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Components

#1: Protein ATP sulfurylase from Methanothermococcus thermolithotrophicus


Mass: 44719.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: /
Source: (gene. exp.) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Strain: DSM 2095 / Tissue: / / Cell: / / Cell line: / / Gene: sat / Organ: / / Variant: / / Plasmid: pET-28a(+)
Details (production host): The synthetic gene was cloned in pET-28a(+) by using the restriction sites NdeI and BamHI with a stop codon (TGA) incorporated before BamHI
Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Tissue (production host): / / Variant (production host): / / References: sulfate adenylyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.8 Å3/Da / Density % sol: 67.61 % / Description: transparent, star-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Purified ATPS sulfurylase from Methanothermococcus thermolithotrophicus was concentrated to 14 mg.ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, and 150 mM NaCl. ...Details: Purified ATPS sulfurylase from Methanothermococcus thermolithotrophicus was concentrated to 14 mg.ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, and 150 mM NaCl. Crystals were obtained by mixing 0.7 ul of the sample with 0.7 ul of 35 % w/v Pentaerythritol ethoxylate (15/4 EO/OH), and 100 mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5 in a 96-Well MRC 2-drop crystallization plates in polystyrene (SWISSCI) containing 90 ul of crystallization solution in the reservoir.
PH range: / / Temp details: 291 +/- 1 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→78.79 Å / Num. obs: 28197 / % possible obs: 93.2 % / Redundancy: 13.7 % / Biso Wilson estimate: 37.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.042 / Rrim(I) all: 0.157 / Net I/σ(I): 12.7
Reflection shellResolution: 1.97→2.22 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.74 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1410 / CC1/2: 0.641 / Rpim(I) all: 0.483 / Rrim(I) all: 1.806 / % possible all: 62.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V47

1v47


Resolution: 1.97→49.73 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.43 / Stereochemistry target values: ML
Details: The final cycles of refinement were performed without hydrogens and by applying translational-liberation screw.
RfactorNum. reflection% reflection
Rfree0.2179 1425 5.06 %
Rwork0.1885 26760 -
obs0.19 28185 58.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.77 Å2 / Biso mean: 42.81 Å2 / Biso min: 22.32 Å2
Refinement stepCycle: final / Resolution: 1.97→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 49 208 3393
Biso mean--62.66 42.98 -
Num. residues----382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.040.4354110.30711561674
2.04-2.120.3672140.275244746110
2.12-2.220.2875340.259778081417
2.22-2.340.2749770.27081434151132
2.34-2.480.2941420.27892467260955
2.48-2.680.27481700.25563346351673
2.68-2.940.26372210.23414062428388
2.94-3.370.23092830.211445344817100
3.37-4.250.19162310.154646924923100
4.25-49.730.18632420.159748425084100
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)
13.1624-0.2157-0.05923.2976-0.58472.43320.2166-1.0574-0.11270.498-0.2892-0.0245-0.1170.89-0.04110.3385-0.0715-0.09970.4884-0.11050.283465.4835.6968194.7364
22.03860.5437-0.65870.77460.18581.82990.0287-0.31350.05920.0540.03570.2228-0.00790.160900.27830.03530.02140.3481-0.11550.32953.75534.2902187.8618
31.3192-0.82130.43421.25780.57721.9211-0.1346-0.03680.2116-0.0220.05570.16410.1127-0.16390.00110.22020.01940.00020.2215-0.09620.25749.606337.5515184.4436
41.3554-0.1334-1.01231.0728-0.10472.9293-0.1018-0.094-0.004-0.02560.02010.13790.085-0.093500.2693-0.01590.01430.272-0.07420.308450.733729.7363184.9461
50.353-0.7946-0.64532.99781.22592.2578-0.1061-0.41860.16820.03930.09980.20410.0780.0922-0.00070.25160.0244-0.00160.3155-0.0260.276373.961522.0615174.8254
60.3982-0.8651-0.2941.88730.52250.7145-0.224-0.3088-0.0870.38380.140.10430.14990.0706-0.00040.25570.03070.03940.2271-0.00380.171470.029921.2942176.6896
70.442-0.38480.06780.3383-0.05020.0121-0.11250.2745-0.2796-0.3243-0.12690.36220.4426-0.6997-0.11770.4176-0.1904-0.02750.5577-0.17440.413863.226526.7259166.4561
80.2178-0.4791-0.43961.0130.90860.81640.10310.00160.1455-0.0466-0.16460.1063-0.1525-0.132300.28570.02420.01450.33890.00610.302971.722421.9979156.7596
91.04830.50820.58661.92640.74771.6346-0.0497-0.0152-0.34190.26570.01550.52010.126-0.12340.00260.28710.02890.09720.23480.04950.381968.85153.2836170.5018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 69 )A26 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 97 )A70 - 97
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 170 )A98 - 170
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 228 )A171 - 228
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 275 )A229 - 275
7X-RAY DIFFRACTION7chain 'A' and (resid 276 through 297 )A276 - 297
8X-RAY DIFFRACTION8chain 'A' and (resid 298 through 345 )A298 - 345
9X-RAY DIFFRACTION9chain 'A' and (resid 346 through 382 )A346 - 382

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