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Basic information

Entry
Database: PDB / ID: 1lm1
TitleStructural studies on the synchronization of catalytic centers in glutamate synthase: native enzyme
ComponentsFerredoxin-dependent glutamate synthase
KeywordsOXIDOREDUCTASE / glutamate synthase / channeling / amidotransferase
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
ACETATE ION / FE3-S4 CLUSTER / FLAVIN MONONUCLEOTIDE / Ferredoxin-dependent glutamate synthase 2
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Authorsvan Den Heuvel, R.H. / Ferrari, D. / Bossi, R.T. / Ravasio, S. / Curti, B. / Vanoni, M.A. / Florencio, F.J. / Mattevi, A.
CitationJournal: J.BIOL.CHEM. / Year: 2002
Title: Structural studies on the synchronization of catalytic centers in glutamate synthase
Authors: van Den Heuvel, R.H. / Ferrari, D. / Bossi, R.T. / Ravasio, S. / Curti, B. / Vanoni, M.A. / Florencio, F.J. / Mattevi, A.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,5825
Polymers165,7121
Non-polymers8704
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.083, 166.083, 219.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ferredoxin-dependent glutamate synthase


Mass: 165711.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: pcc6803 / Production host: Escherichia coli (E. coli)
References: UniProt: P55038, glutamate synthase (ferredoxin)
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 4.57 Å3/Da / Density % sol: 73.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlenzyme1drop
225 mMPIPES-KOH1droppH7.0
31 mMEDTA1drop
410 %glycerol1drop
524-30 %(w/v)PEG40001reservoir
6100 mMTris-HCl1reservoirpH8.5
7200 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2001
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→62 Å / Num. all: 76995 / Num. obs: 76995 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 3.8
Reflection shellResolution: 2.8→2.94 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.7 / Num. unique all: 10697 / Rsym value: 0.512 / % possible all: 96.6
Reflection
*PLUS
Lowest resolution: 62 Å / Num. measured all: 1595358 / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.455

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.06refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA0

1ea0


Resolution: 2.8→129.1 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.891 / SU B: 15.102 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.424 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28677 1869 2.5 %RANDOM
Rwork0.23638 ---
all0.2376 73899 --
obs0.23764 73899 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.074 Å2
Baniso -1Baniso -2Baniso -3
1-4.2 Å20 Å20 Å2
2--4.2 Å20 Å2
3----8.39 Å2
Refinement stepCycle: LAST / Resolution: 2.8→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11311 0 46 38 11395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02111581
X-RAY DIFFRACTIONr_angle_refined_deg2.2281.96615704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.27851471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.26517.0933344
X-RAY DIFFRACTIONr_chiral_restr0.1650.21751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028798
X-RAY DIFFRACTIONr_nbd_refined0.3280.26809
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2549
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3510.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.26
X-RAY DIFFRACTIONr_mcbond_it0.7451.57308
X-RAY DIFFRACTIONr_mcangle_it1.341211707
X-RAY DIFFRACTIONr_scbond_it2.29634273
X-RAY DIFFRACTIONr_scangle_it3.614.53994
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.382 123
Rwork0.349 5305
obs-5305
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)
11.821-1.1164-1.76661.4630.84493.07480.13470.6004-0.2034-0.2167-0.50590.21660.133-0.73940.37110.12570.085-0.04790.5918-0.12210.3384178.7002208.6651-9.1326
22.2413-0.1829-0.53551.49570.23722.3963-0.2557-0.011-0.43990.5855-0.2160.48570.9981-0.47570.47170.4183-0.31790.36170.2715-0.18360.5907164.4424199.701928.9391
31.6991-0.9061-0.90381.8811.0372.7867-0.1126-0.4170.18030.56810.2095-0.19580.11530.5644-0.09690.0969-0.0699-0.00120.3147-0.0330.244188.9654223.19434.4415
42.0422-0.8981-0.42541.8930.47063.13190.50350.41440.4278-0.5327-0.36220.0616-1.2029-0.609-0.14130.49950.24310.15020.32760.05150.3887174.0339240.29367.7455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4221 - 422
2X-RAY DIFFRACTION2AA439 - 779439 - 779
3X-RAY DIFFRACTION3AA780 - 1223780 - 1223
4X-RAY DIFFRACTION4AA1224 - 15031224 - 1503
Refinement
*PLUS
Rfactor Rfree: 0.287 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.23

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