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- PDB-1ofe: Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglu... -

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Basic information

Entry
Database: PDB / ID: 1ofe
TitleGlutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate and L-DON at 2.45 Angstrom resolution
ComponentsFERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2
KeywordsOXIDOREDUCTASE / COMPLEX ENZYME / SUBSTRATE CHANNELING / AMIDOTRANSFERASE / FLAVOPROTEIN / IRON-SULPHUR / FD-GOGAT
Function / homology
Function and homology information


glutamate synthase (ferredoxin) / glutamate synthase (NADH) activity / glutamate synthase (ferredoxin) activity / ammonia assimilation cycle / L-glutamate biosynthetic process / glutamate biosynthetic process / 3 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Glutamate synthase, alpha subunit, C-terminal domain / Glutamate synthase domain / Glutamate synthase, central-N / Glutamine amidotransferases class-II / Conserved region in glutamate synthase / Glutamate synthase central domain / Glutamate synthase, alpha subunit, C-terminal / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Glutamine amidotransferase type 2 domain profile. ...Glutamate synthase, alpha subunit, C-terminal domain / Glutamate synthase domain / Glutamate synthase, central-N / Glutamine amidotransferases class-II / Conserved region in glutamate synthase / Glutamate synthase central domain / Glutamate synthase, alpha subunit, C-terminal / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Pectate Lyase C-like / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 3 Solenoid / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / FE3-S4 CLUSTER / FLAVIN MONONUCLEOTIDE / 5-OXO-L-NORLEUCINE / Ferredoxin-dependent glutamate synthase 2
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsVan Den heuvel, R.H.H. / Mattevi, A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Active Conformation of Glutamate Synthase and its Binding to Ferredoxin
Authors: Van Den Heuvel, R.H.H. / Svergun, D.I. / Petoukhov, M.V. / Coda, A. / Curti, B. / Ravasio, S. / Vanoni, M.A. / Mattevi, A.
History
DepositionApr 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2
B: FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,51010
Polymers331,4232
Non-polymers2,0878
Water5,206289
1
A: FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7555
Polymers165,7121
Non-polymers1,0434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7555
Polymers165,7121
Non-polymers1,0434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.669, 134.377, 198.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97162, -0.23589, 0.01751), (0.23638, 0.96549, -0.10935), (0.00889, 0.11039, 0.99385)
Vector: 67.42299, 66.47877, -2.1723)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2 / GLUTAMATE SYNTHASE


Mass: 165711.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC6803 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CLR207 RECA
References: UniProt: P55038, glutamate synthase (ferredoxin)

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Non-polymers , 5 types, 297 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-ONL / 5-OXO-L-NORLEUCINE


Type: L-peptide linking / Mass: 145.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYSES THE REACTION 2 L-GLUTAMATE + 2 OXIDIZED FERREDOXIN TO L-GLUTAMINE + 2-OXOGLUTARATE + 2 ...CATALYSES THE REACTION 2 L-GLUTAMATE + 2 OXIDIZED FERREDOXIN TO L-GLUTAMINE + 2-OXOGLUTARATE + 2 REDUCED FERREDOXIN. ALSO BINDS FAD,FMN AND A 3FE-4S CLUSTER

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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: 2.47 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein1drop
220 mMHEPES-KOH1drop
310 %(v/v)glycerol1drop
42 mM2-OG1drop
55 mMdithiothreitol1droppH7.5
620-26 %(w/v)PEG40001reservoir
7100 Tris-HCl1reservoir
8200 mMsodium acetate1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 120397 / % possible obs: 99.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.113
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.306 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 111.8 Å / % possible obs: 99.5 % / Num. measured all: 1066424 / Rmerge(I) obs: 0.113
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LLW

1llw


Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 10.655 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.537 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.257 6044 5 %RANDOM
Rwork0.207 ---
obs0.209 114152 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET
Displacement parametersBiso mean: 17.2 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22776 0 116 289 23181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02123340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9731640
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17452960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31428.5433856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.96917.0936738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.52315140
X-RAY DIFFRACTIONr_chiral_restr0.120.23534
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217714
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.210595
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2847
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5641.514712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.043223578
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96738628
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0664.58056
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 438
Rwork0.258 8366
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)
11.83130.21660.61060.78050.08581.09920.1434-0.1852-0.37070.0616-0.0276-0.06360.10170.1618-0.11590.11770.0933-0.04170.27630.11420.174439.03219.31227.565
22.83390.42360.10780.74260.19460.99990.1175-0.3866-0.85360.0853-0.05680.05970.2959-0.1492-0.06070.20410.0016-0.06080.17990.24520.3827-0.8046.8924.344
31.9850.08470.31490.8048-0.03271.33510.0697-0.52130.3780.1208-0.04610.212-0.0577-0.216-0.02370.08810.05820.01730.2789-0.09630.1527-1.61142.53427.44
42.3812-0.0096-0.07541.31770.54481.45920.01190.29010.2377-0.26210.0001-0.07-0.0810.1016-0.0120.11040.04350.01090.20040.09860.049624.01140.867-0.228
51.81650.34010.32350.99430.39681.55550.2270.0978-0.2144-0.2048-0.16160.02180.00630.3422-0.06550.28640.2645-0.04310.4689-0.05420.081101.26891.35327.717
61.46090.1336-0.03741.22490.10491.340.0030.0279-0.4154-0.0703-0.08210.15680.4506-0.17470.07910.43870.2174-0.19360.3727-0.18960.371865.39970.2322.803
72.08150.12230.15721.1346-0.34141.6920.2849-0.00850.2338-0.0835-0.16920.4211-0.0359-0.2559-0.11570.2920.2486-0.13080.3497-0.19050.283156.286104.16729.824
81.79470.2442-0.57191.43310.45441.63150.16340.60620.2961-0.5203-0.06760.0834-0.30880.0759-0.09580.65540.3763-0.08510.55710.08750.193481.076111.5742.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 422
2X-RAY DIFFRACTION2A423 - 786
3X-RAY DIFFRACTION3A787 - 1239
4X-RAY DIFFRACTION4A1240 - 1507
5X-RAY DIFFRACTION5B1 - 422
6X-RAY DIFFRACTION6B423 - 786
7X-RAY DIFFRACTION7B787 - 1239
8X-RAY DIFFRACTION8B1240 - 1507
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.79

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