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- PDB-8oox: Glutamine synthetase from Methermicoccus shengliensis at a resolu... -

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Basic information

Entry
Database: PDB / ID: 8oox
TitleGlutamine synthetase from Methermicoccus shengliensis at a resolution of 3.09 A
ComponentsGlutamine synthetase
KeywordsLIGASE / Nitrogen-assimilation / methanogenic archaea / methylotrophic / thermophile / ammonia / glutamate / ATP
Function / homology
Function and homology information


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Glutamine synthetase type I / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily ...Glutamine synthetase type I / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
CITRIC ACID / Glutamine synthetase
Similarity search - Component
Biological speciesMethermicoccus shengliensis DSM 18856 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsMueller, M.-C. / Lemaire, O.N. / 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 6, 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
B: Glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,15812
Polymers99,1732
Non-polymers98510
Water0
1
A: Glutamine synthetase
B: Glutamine synthetase
hetero molecules
x 6


  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
  • 601 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)600,94972
Polymers595,03712
Non-polymers5,91360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation14_555-y+1/4,-x+1/4,-z+1/41
crystal symmetry operation18_454-x-1/4,z+1/4,y-1/41
crystal symmetry operation22_455z-1/4,-y+3/4,x+1/41
Buried area77830 Å2
ΔGint-381 kcal/mol
Surface area181040 Å2
Unit cell
Length a, b, c (Å)226.465, 226.465, 226.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Glutamine synthetase /


Mass: 49586.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methermicoccus shengliensis DSM 18856 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 18856 / Tissue: / / References: UniProt: A0A832VZP6
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN

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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: 4.89 Å3/Da / Density % sol: 74.84 % / Description: Flat squares
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: The protein was crystallized fresh without any freezing step, and obtained through the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI, United ...Details: The protein was crystallized fresh without any freezing step, and obtained 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). Crystallization was performed at 9 mg/ml glutamine synthetase in 25 mM Tris/HCl pH 7.6, 10% glycerol, and 2 mM dithiothreitol. The reservoir contained 90 ul precipitant (1.6 M sodium citrate tribasic dihydrate). 0.55 uL protein was mixed with 0.55 uL precipitant. Crystals were soaked in the precipitant supplemented with 30% v/v glycerol before 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: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 3.088→130.75 Å / Num. obs: 35711 / % possible obs: 96.6 % / Redundancy: 26.6 % / Biso Wilson estimate: 83.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.068 / Rrim(I) all: 0.352 / Net I/σ(I): 12.2
Reflection shellResolution: 3.088→3.172 Å / Redundancy: 26.8 % / Rmerge(I) obs: 3.099 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1793 / CC1/2: 0.486 / Rpim(I) all: 0.607 / Rrim(I) all: 3.159 / % possible all: 63.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→65.37 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.81 / Stereochemistry target values: ML
Details: Refinement was performed with PHENIX and BUSTER in combination with fast automatic visual model building in COOT. All models were systematically validated by using Molprobity. The model was ...Details: Refinement was performed with PHENIX and BUSTER in combination with fast automatic visual model building in COOT. All models were systematically validated by using Molprobity. The model was refined by applying Translation/Libration/Screw, without Non-crystallographic symmetry and without generating hydrogens.
RfactorNum. reflection% reflection
Rfree0.2162 1748 4.9 %
Rwork0.1863 --
obs0.1878 35696 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→65.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 64 0 6984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047134
X-RAY DIFFRACTIONf_angle_d0.6789661
X-RAY DIFFRACTIONf_dihedral_angle_d16.182691
X-RAY DIFFRACTIONf_chiral_restr0.0451047
X-RAY DIFFRACTIONf_plane_restr0.0131272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.180.3225870.27091858X-RAY DIFFRACTION65
3.18-3.280.30791370.26542695X-RAY DIFFRACTION94
3.28-3.40.29071340.24752881X-RAY DIFFRACTION100
3.4-3.530.25931600.2372863X-RAY DIFFRACTION100
3.53-3.70.28031780.20832856X-RAY DIFFRACTION100
3.7-3.890.23811490.18482897X-RAY DIFFRACTION100
3.89-4.130.18881410.16012906X-RAY DIFFRACTION100
4.13-4.450.17621380.15372922X-RAY DIFFRACTION100
4.45-4.90.18541570.14192929X-RAY DIFFRACTION100
4.9-5.610.16271560.16872954X-RAY DIFFRACTION100
5.61-7.060.25611380.2113013X-RAY DIFFRACTION100
7.07-65.370.19611730.18013174X-RAY DIFFRACTION100
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)
13.7298-0.157-2.19184.974-1.21474.8288-0.1432-0.1642-0.1943-0.13110.16680.54090.4023-0.3205-0.04080.4351-0.0805-0.0810.6316-0.02630.6537-75.899361.131918.1988
22.24420.40350.471.62520.35422.89780.1119-0.1101-0.38540.1903-0.03860.02380.2787-0.0521-0.09420.43110.0546-0.06840.46170.03070.606-56.453448.82949.911
32.69962.2696-0.18053.3925-0.33480.5696-0.1070.1967-0.4338-0.25460.1015-0.21270.09640.07390.01430.6150.0523-0.10060.6207-0.04590.6112-53.680752.1666-5.6582
42.1458-0.1290.47841.4556-0.06561.56460.0313-0.0755-0.2667-0.05760.08290.22540.2433-0.2059-0.10260.50170.0013-0.0460.43490.06620.6104-32.499135.612927.9622
50.95990.7257-0.56534.4971-1.44061.47560.1072-0.0917-0.2649-0.0772-0.1389-0.42280.27860.23850.02450.49580.1126-0.08410.5149-0.02690.5983-12.017233.74718.7418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 107 )
2X-RAY DIFFRACTION2chain 'B' and (resid 108 through 295 )
3X-RAY DIFFRACTION3chain 'B' and (resid 296 through 442 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3 through 266 )
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 442 )

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