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- PDB-9x50: Crystal structure of Fgm3 in complex with PLP and L-Ala -

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Basic information

Entry
Database: PDB / ID: 9x50
TitleCrystal structure of Fgm3 in complex with PLP and L-Ala
ComponentsAminotransferase-like protein FGM3
KeywordsBIOSYNTHETIC PROTEIN / PLP / Retro-aldol-like / Cbeta-Cgamma Bond Cleavage
Function / homologyTransferases / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / transferase activity / Chem-0JO / Aminotransferase-like protein FGM3
Function and homology information
Biological speciesFusarium graminearum PH-1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, H. / Xia, M. / Fang, P. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22522706 China
CitationJournal: Acs Catalysis / Year: 2026
Title: Structural and Mechanistic Insights into Fgm3-Catalyzed C beta-C gamma Bond Cleavage of an Amino Acid
Authors: Zhang, H. / Xia, M. / Mu, X. / Fang, P. / Tang, Z. / Liu, W.
History
DepositionOct 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase-like protein FGM3
B: Aminotransferase-like protein FGM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4876
Polymers89,6712
Non-polymers8174
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-25 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.803, 98.013, 69.827
Angle α, β, γ (deg.)90.00, 116.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aminotransferase-like protein FGM3 / C64 cluster protein NRPS5 / Fg3_54 cluster protein FGM3 / Fusaoctaxin A biosynthesis cluster protein FGM3


Mass: 44835.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium graminearum PH-1 (fungus) / Gene: FGM3, FGRAMPH1_01T20965 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C3YKE0, Transferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES, 6.25 % w/v PEG 2000, 6.25 % w/v PEG 3350, 6.25 % w/v PEG 4000, 6.25 % w/v PEG 5000 MME, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→38.58 Å / Num. obs: 47945 / % possible obs: 97.5 % / Redundancy: 2.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.054 / Rrim(I) all: 0.08 / Χ2: 0.52 / Net I/σ(I): 8.8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.153 / Num. unique obs: 3524 / CC1/2: 0.932 / Rpim(I) all: 0.152 / Rrim(I) all: 0.216 / Χ2: 0.75

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.81 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1873 2003 4.19 %
Rwork0.1513 --
obs0.1528 47835 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 54 621 6791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086297
X-RAY DIFFRACTIONf_angle_d0.8918583
X-RAY DIFFRACTIONf_dihedral_angle_d6.322872
X-RAY DIFFRACTIONf_chiral_restr0.053996
X-RAY DIFFRACTIONf_plane_restr0.0071103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.23071300.16312932X-RAY DIFFRACTION87
2.15-2.210.22331300.16453123X-RAY DIFFRACTION94
2.21-2.280.2431350.17653165X-RAY DIFFRACTION93
2.28-2.350.19561520.15333302X-RAY DIFFRACTION100
2.35-2.430.20661380.15083338X-RAY DIFFRACTION100
2.43-2.530.2091440.15173356X-RAY DIFFRACTION100
2.53-2.650.2311600.15843344X-RAY DIFFRACTION100
2.65-2.780.21351490.15643307X-RAY DIFFRACTION98
2.79-2.960.19861490.153347X-RAY DIFFRACTION100
2.96-3.190.18141500.15643341X-RAY DIFFRACTION99
3.19-3.510.18561470.14783297X-RAY DIFFRACTION98
3.51-4.020.15331390.13723266X-RAY DIFFRACTION97
4.02-5.060.1381490.13283349X-RAY DIFFRACTION99
5.06-36.810.1631310.16033365X-RAY DIFFRACTION97

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