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- PDB-1ea0: Alpha subunit of A. brasilense glutamate synthase -

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Basic information

Entry
Database: PDB / ID: 1ea0
TitleAlpha subunit of A. brasilense glutamate synthase
ComponentsGLUTAMATE SYNTHASE [NADPH] LARGE CHAIN
KeywordsOXIDOREDUCTASE / IRON SULPHUR FLAVOPROTEIN
Function / homology
Function and homology information


glutamate synthase (NADPH) / glutamate synthase (NADPH) activity / L-glutamate biosynthetic process / 3 iron, 4 sulfur cluster binding / glutamine metabolic process / 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 / S-DIOXYMETHIONINE / Glutamate synthase [NADPH] large chain
Similarity search - Component
Biological speciesAZOSPIRILLUM BRASILENSE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsBinda, C. / Bossi, R.T. / Vanoni, M.A. / Mattevi, A.
CitationJournal: Structure / Year: 2000
Title: Cross-Talk and Ammonia Channeling between Active Centers in the Unexpected Domain Arrangement of Glutamate Synthase
Authors: Binda, C. / Bossi, R.T. / Wakatsuki, S. / Arzt, S. / Coda, A. / Curti, B. / Vanoni, M.A. / Mattevi, A.
History
DepositionNov 2, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AK" IN CHAIN A AND "BH" IN CHAIN B SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AK" IN CHAIN A AND "BH" IN CHAIN B SHEET RECORDS BELOW ARE ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN
B: GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,78610
Polymers324,6272
Non-polymers2,1598
Water0
1
A: GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,3935
Polymers162,3141
Non-polymers1,0794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,3935
Polymers162,3141
Non-polymers1,0794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)233.612, 233.612, 305.089
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.903004, 0.248079, 0.35077), (0.244558, -0.374459, 0.894411), (0.353234, 0.893441, 0.277468)
Vector: 69.996, 44.252, -50.282)
DetailsGLUTAMATE SYNTHASE IS FUNCTIONAL AS A HETERODIMER MADE UPOF ONE ALPHA AND ONE BETA SUBUNIT. THE STRUCTURE PRESENTEDHERE, OF THE ALPHA SUBUNIT ON ITS OWN, IS MONOMERIC.

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Components

#1: Protein GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN / GLUTAMATE SYNTHASE ALPHA SUBUNIT / NADPH-GOGAT / GLTS ALPHA CHAIN


Mass: 162313.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AZOSPIRILLUM BRASILENSE (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05755, glutamate synthase (NADPH)
#2: Chemical ChemComp-OMT / S-DIOXYMETHIONINE


Type: L-peptide linking / Mass: 181.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO4S
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
Compound details2 L-GLUTAMATE + NADP(+) = L-GLUTAMINE + 2-OXOGLUTARATE + NADPH. BINDS A 3FE-4S CLUSTER, FAD AND FMN.

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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 % sol: 83 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 mg/mlprotein1drop
21 mMEDTA1drop
310 %(v/v)glycerol1drop
42 mMMetS1drop
52 mM2-oxoglutarate1drop
62 mMAADP1drop
75 mMdithiothreitol1drop
825 mMHEPES1drop
920 %(v/v)tert-butanol1reservoir
1015 %(w/v)PEG33501reservoir
11100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.993
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 184182 / % possible obs: 98.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 6.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.456 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 758585
Reflection shell
*PLUS
% possible obs: 94.1 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / SU B: 11.366 / SU ML: 0.2091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38594 / ESU R Free: 0.3079
RfactorNum. reflection% reflectionSelection details
Rfree0.28712 1847 1 %RANDOM
Rwork0.25587 ---
obs0.25618 181808 98.6 %-
Displacement parametersBiso mean: 57.963 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0.92 Å20 Å2
2---1.84 Å20 Å2
3---2.77 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22360 0 118 0 22478
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.021
X-RAY DIFFRACTIONp_angle_d0.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8151.5
X-RAY DIFFRACTIONp_mcangle_it4.8882
X-RAY DIFFRACTIONp_scbond_it8.4093
X-RAY DIFFRACTIONp_scangle_it13.4494.5
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.2240.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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