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- PDB-8a8d: ATP sulfurylase from Methanothermococcus thermolithotrophicus - m... -

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Basic information

Entry
Database: PDB / ID: 8a8d
TitleATP sulfurylase from Methanothermococcus thermolithotrophicus - monoclinic form
ComponentsATP sulfurylase from Methanothermococcus thermolithotrophicus
KeywordsTRANSFERASE / Sulfate-assimilation / methanogens / archaea / APS / thermophile / methane / ATP / activation / marine / pyrophosphate
Function / homologySulfate adenylyltransferase / Sulfate adenylyltransferase / HUPs / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 22, 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

Downloads & links

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Assembly

Deposited unit
A: ATP sulfurylase from Methanothermococcus thermolithotrophicus
B: ATP sulfurylase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,68521
Polymers89,4402
Non-polymers1,24619
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Confirmed by gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.282, 54.525, 85.430
Angle α, β, γ (deg.)90.000, 95.910, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP sulfurylase from Methanothermococcus thermolithotrophicus


Mass: 44719.762 Da / Num. of mol.: 2
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: pET28a(+)
Details (production host): Synthetic gene was cloned in pET28a(+) 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

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Non-polymers , 6 types, 373 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.85 %
Description: Transparent, long but thin plate-shaped crystals appeared after a few weeks
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MtATPS in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol (0.7 ul) at a concentration of 27 mg.ml-1 was mixed with 0.7 ul reservoir solution. Crystals were obtained in the following crystallization ...Details: MtATPS in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol (0.7 ul) at a concentration of 27 mg.ml-1 was mixed with 0.7 ul reservoir solution. Crystals were obtained in the following crystallization condition: 20 % w/v polyethylene glycol 8000, 100 mM MES pH 6.0 and 200 mM Calcium acetate.
PH range: / / Temp details: 291 K +/- 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: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→65.94 Å / Num. obs: 41069 / % possible obs: 95.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.055 / Rrim(I) all: 0.146 / Net I/σ(I): 10.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.149 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2053 / CC1/2: 0.57 / Rpim(I) all: 0.475 / Rrim(I) all: 1.246 / % possible all: 98.3

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Processing

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

1v47


Resolution: 2.1→52.28 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
Details: The final cycles of refinement were performed with hydrogens in riding position, without applying non-crystallography symmetry and with translational-liberation screw.
RfactorNum. reflection% reflection
Rfree0.2394 2096 5.11 %
Rwork0.1986 38961 -
obs0.2007 41057 82.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.56 Å2 / Biso mean: 39.0955 Å2 / Biso min: 17.47 Å2
Refinement stepCycle: final / Resolution: 2.1→52.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6205 0 71 354 6630
Biso mean--53.51 38.52 -
Num. residues----753
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.342820.26521590167251
2.15-2.20.2759890.2671707179655
2.2-2.260.29931250.24931830195559
2.26-2.330.2909980.23681973207163
2.33-2.40.24531040.23872148225268
2.4-2.490.27861450.23332360250575
2.49-2.590.29081210.23912578269982
2.59-2.710.27891550.23572760291588
2.71-2.850.26621730.21342958313194
2.85-3.030.26661670.2143087325498
3.03-3.260.28931660.212931343300100
3.26-3.590.22061580.183131753333100
3.59-4.110.21770.164931733350100
4.11-5.180.17051590.149132053364100
5.18-52.280.23721770.207132833460100
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)
11.70640.1525-0.10351.3212-0.03911.4370.0208-0.1357-0.260.1732-0.0275-0.05740.08420.0697-0.00080.16950.01430.02110.220.03870.273165.45097.011334.3775
22.22111.6166-1.32951.3941-0.59931.611-0.03040.122-0.09570.0840.07910.0618-0.0493-0.1634-0.06590.21360.06570.01890.23950.05310.288671.761721.948718.1176
31.7431-0.26840.83180.6811-0.97733.1428-0.0961-0.0519-0.2406-0.0076-0.0167-0.06920.11720.06420.05990.2471-0.00780.010.1410.01510.308286.317223.86165.6829
42.8538-0.1357-0.07854.2010.58511.9677-0.0320.68640.1543-0.81360.2370.3883-0.1454-0.6806-0.1620.28920.0026-0.0930.56680.0680.34253.086860.351-34.0374
51.4225-0.4201-0.44791.90460.2261.24360.14330.18510.3844-0.0435-0.06270.0923-0.1477-0.2349-0.06330.19790.0016-0.04560.3010.10040.374755.786765.0951-20.6906
62.8512-1.2140.54690.5362-0.47242.34170.02510.15770.1405-0.08260.04570.09590.0148-0.0652-0.08610.1815-0.0336-0.01260.1830.04840.274671.141946.1235-13.6372
71.7669-2.04940.96062.4836-1.57582.3504-0.3388-0.1830.32340.50660.19240.0765-0.1776-0.03540.19460.2931-0.0076-0.01640.30940.06320.421160.21953.1518-4.2065
81.48230.0919-0.42170.9218-0.47992.88380.05970.06190.15550.0688-0.0312-0.0976-0.3315-0.0159-0.0410.19420.00040.00010.14830.01220.271884.772647.5465-3.3557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 181 )A2 - 181
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 319 )A182 - 319
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 382 )A320 - 382
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 36 )B3 - 36
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 180 )B37 - 180
6X-RAY DIFFRACTION6chain 'B' and (resid 181 through 261 )B181 - 261
7X-RAY DIFFRACTION7chain 'B' and (resid 262 through 319 )B262 - 319
8X-RAY DIFFRACTION8chain 'B' and (resid 320 through 382 )B320 - 382

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