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- PDB-8ooo: Glutamine synthetase from Methanothermococcus thermolithotrophicu... -

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Basic information

Entry
Database: PDB / ID: 8ooo
TitleGlutamine synthetase from Methanothermococcus thermolithotrophicus in complex with 2-oxoglutarate and MgATP at 2.15 A resolution
ComponentsGlutamine synthetase from Methanothermococcus thermolithotrophicus
KeywordsLIGASE / Nitrogen-assimilation / methanogenic archaea / allosteric activation / hydrogenotrophic / thermophile / marine / 2-oxoglutarate / glutamate / ATP / allosteric binding site
Function / homology2-OXOGLUTARIC ACID / ADENOSINE-5'-TRIPHOSPHATE / METHOXY-ETHOXYL / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å
AuthorsMueller, M.-C. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Societyna Germany
German Research Foundation (DFG)KU 3768/1-1 Germany
CitationJournal: Commun Biol / Year: 2024
Title: Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations.
Authors: Muller, M.C. / Lemaire, O.N. / Kurth, J.M. / Welte, C.U. / Wagner, T.
History
DepositionApr 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine synthetase from Methanothermococcus thermolithotrophicus
B: Glutamine synthetase from Methanothermococcus thermolithotrophicus
C: Glutamine synthetase from Methanothermococcus thermolithotrophicus
D: Glutamine synthetase from Methanothermococcus thermolithotrophicus
E: Glutamine synthetase from Methanothermococcus thermolithotrophicus
F: Glutamine synthetase from Methanothermococcus thermolithotrophicus
G: Glutamine synthetase from Methanothermococcus thermolithotrophicus
H: Glutamine synthetase from Methanothermococcus thermolithotrophicus
I: Glutamine synthetase from Methanothermococcus thermolithotrophicus
J: Glutamine synthetase from Methanothermococcus thermolithotrophicus
K: Glutamine synthetase from Methanothermococcus thermolithotrophicus
L: Glutamine synthetase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)614,77080
Polymers603,55212
Non-polymers11,21868
Water54,7843041
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area83270 Å2
ΔGint-148 kcal/mol
Surface area186160 Å2
Unit cell
Length a, b, c (Å)112.337, 131.773, 131.507
Angle α, β, γ (deg.)60.04, 87.72, 67.34
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Glutamine synthetase from Methanothermococcus thermolithotrophicus


Mass: 50296.039 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: glutamine synthetase

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Non-polymers , 9 types, 3109 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MOE / METHOXY-ETHOXYL


Mass: 75.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O2
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3041 / 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: 2.53 Å3/Da / Density % sol: 51.5 % / Description: Short thick hexagonal rod
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: The enzyme was crystallized at 3.7 mg/ml with a final concentration of 2 mM sodium 2-oxoglutarate, 2 mM ATP and 2 mM MgCl in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 150 mM NaCl, 2 mM ...Details: The enzyme was crystallized at 3.7 mg/ml with a final concentration of 2 mM sodium 2-oxoglutarate, 2 mM ATP and 2 mM MgCl in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 150 mM NaCl, 2 mM dithiothreitol. The protein was crystallized fresh without any freezing step, and crystallization was performed through the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI, United Kingdom) under anaerobic conditions (N2:H2, gas ratio of 97:3). The crystallization reservoir contained 90 ul of mother liquor (20 % w/v polyethylene glycol 3,350 and 200 mM sodium fluoride). The crystallization drop contained 0.6 ul protein with ligands and 0.6 ul precipitant. Crystals were soaked in the mother liquor supplemented with 20 % v/v glycerol prior to freezing in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.30511 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30511 Å / Relative weight: 1
ReflectionResolution: 2.148→110.034 Å / Num. obs: 248419 / % possible obs: 92.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.99 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.068 / Rrim(I) all: 0.13 / Net I/σ(I): 9.3
Reflection shellResolution: 2.148→2.297 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 12420 / CC1/2: 0.569 / Rpim(I) all: 0.59 / Rrim(I) all: 1.122 / % possible all: 58.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.149→42.88 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.361 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.365 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.216
Details: The structure was refined in BUSTER by applying non crystallography symmetry and translation libration screw model.
RfactorNum. reflection% reflection
Rfree0.214 12081 4.86 %
Rwork0.1816 --
obs0.1832 248376 77 %
Displacement parametersBiso mean: 38.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.6437 Å2-0.219 Å2-0.5019 Å2
2--0.383 Å20.1911 Å2
3---0.2608 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.149→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42408 0 710 3041 46159
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00944178HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9359834HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d15235SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes7464HARMONIC5
X-RAY DIFFRACTIONt_it44178HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.73
X-RAY DIFFRACTIONt_other_torsion16.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5580SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact38983SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.24 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3001 269 5.41 %
Rwork0.2648 4699 -
all0.2667 4968 -
obs--12.73 %
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)
10.32840.0211-0.03550.3213-0.16930.17480.0192-0.0184-0.0634-0.04770.01230.05420.0159-0.042-0.0315-0.0345-0.0519-0.0347-0.00090.0047-0.0006-32.7819-27.6944-26.0298
20.2819-0.0509-0.06470.0562-0.02160.4346-0.0165-0.06550.0183-0.00120.0443-0.0071-0.05260.0642-0.0279-0.039-0.0285-0.00650.0115-0.04-0.006232.759127.749625.903
30.1794-0.0367-0.01880.17230.14130.3948-0.00260.0312-0.0138-0.0514-0.0150.0091-0.1226-0.02870.01760.06770.0218-0.0205-0.07450.0212-0.0196-4.601942.6732-25.9641
40.26990.0698-0.03840.3349-0.13890.1726-0.00130.04670.0202-0.0446-0.0127-0.03710.01690.05340.014-0.03270.00770.03680.00070.0065-0.001629.606-12.1139-38.4015
50.2779-0.10440.01390.0933-0.0290.46490.03620.0543-0.01030.0126-0.01470.01260.08890.0495-0.02150.00480.005-0.0208-0.0353-0.0107-0.0111.8077-45.7636-16.7473
60.249-0.06240.00020.28250.20480.2347-0.0121-0.02280.0414-0.0540.0328-0.0557-0.04610.0336-0.0207-0.0365-0.05380.0432-0.0218-0.00440.028240.011124.6626-17.1142
70.37430.08860.14350.17770.20490.30550.0398-0.0008-0.05380.05170.0024-0.01880.08540.0095-0.04230.04630.0177-0.0318-0.05050.043-0.02794.4007-42.601326.2705
80.39340.0723-0.01440.2745-0.04470.24830.0084-0.1026-0.0886-0.00260.0164-0.01370.00440.0325-0.0248-0.04020.0078-0.04390.02640.0274-0.026114.9194-5.803447.7626
90.22360.0905-0.02740.1915-0.12610.31690.01410.01120.02250.0178-0.01880.0106-0.1108-0.03530.00470.02920.05010.0008-0.0576-0.03030.0008-11.936145.53517.0664
100.3243-0.04260.11680.3150.09230.1537-0.0090.0327-0.054-0.0456-0.01010.0023-0.0495-0.02070.0191-0.0020.0001-0.0226-0.010.0149-0.0275-14.76015.925-47.6287
110.2870.05420.05210.29560.16470.23390.0154-0.05680.06720.0396-0.05430.010.004-0.06980.0388-0.0570.00080.01380.0481-0.0229-0.026-29.786111.912838.6814
120.2074-0.06980.04050.05890.02780.5428-0.0311-0.05970.0050.0080.03270.00020.0702-0.1205-0.0015-0.0555-0.06140.00680.05250.0249-0.0274-40.2797-24.736917.0747
130.1843-0.07390.06850.0194-0.01990.07070.0057-0.0230.013-0.0231-0.008-0.01840.0035-0.01630.00230.0098-0.0160.0189-0.03650.012-0.05720.08550.1991-0.1982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }

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