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Basic information

Entry
Database: PDB / ID: 1llw
TitleStructural studies on the synchronization of catalytic centers in glutamate synthase: complex with 2-oxoglutarate
ComponentsFerredoxin-dependent glutamate synthase
KeywordsOXIDOREDUCTASE / Ntn amidotransferase / glutamate synthase / chanelling
Function / homology
Function and homology information


glutamate synthase (ferredoxin) / glutamate synthase (ferredoxin) activity / glutamate synthase activity / L-glutamate biosynthetic process / ammonia assimilation cycle / 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 ...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 / Ferredoxin-dependent glutamate synthase 2
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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)166,6104
Polymers165,7121
Non-polymers8983
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.521, 166.521, 219.874
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 4.6 Å3/Da / Density % sol: 73.24 %
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: ID14-1 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2001
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 83666 / Num. obs: 83666 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 4.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.9 / Num. unique all: 11378 / % possible all: 92.1
Reflection
*PLUS
Lowest resolution: 62 Å / Num. measured all: 947721
Reflection shell
*PLUS
% possible obs: 92.7 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.3

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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: 2.7→12 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 14.951 / SU ML: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.371 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29274 2026 2.5 %RANDOM
Rwork0.23447 ---
all0.2359 80245 --
obs0.23591 80245 96.58 %-
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: 41.202 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å20 Å2
2--3.48 Å20 Å2
3----6.95 Å2
Refinement stepCycle: LAST / Resolution: 2.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11311 0 48 49 11408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02111584
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1961.96615709
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.77751471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.12717.0933344
X-RAY DIFFRACTIONr_chiral_restr0.1640.21751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028802
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3140.26785
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2548
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.961.57302
X-RAY DIFFRACTIONr_mcangle_it1.77211703
X-RAY DIFFRACTIONr_scbond_it2.99834282
X-RAY DIFFRACTIONr_scangle_it4.7544.54003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.438 133
Rwork0.373 5306
obs-133
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)
11.3089-0.4997-1.15821.22131.02051.68750.19430.7352-0.1899-0.1511-0.5790.1787-0.0119-0.84140.38470.23410.03920.00540.9357-0.19590.3743179.1709209.0139-9.2124
21.7377-0.4171-0.57431.35750.51111.9715-0.36440.2393-0.42930.5998-0.20340.46120.8397-0.41340.56780.5935-0.42840.48840.357-0.25470.6016164.7198200.34728.8199
31.295-0.8743-0.77721.68690.90612.0827-0.0878-0.15220.26370.47770.1481-0.19770.19470.2465-0.06030.5079-0.06360.00840.5307-0.02580.5401189.2579223.874234.253
41.5448-0.6838-0.58211.46650.80972.75560.52780.47970.3131-0.4271-0.4773-0.1153-0.9908-0.7493-0.05050.44320.32780.16620.54560.10910.3596174.2967240.74977.3986
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: 0.293 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.2
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.77 Å

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