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- PDB-9x4v: Crystal structure of Fgm3 in complex with PLP and L-Arg -

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Basic information

Entry
Database: PDB / ID: 9x4v
TitleCrystal structure of Fgm3 in complex with PLP and L-Arg
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-EQJ / Aminotransferase-like protein FGM3
Function and homology information
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 11, 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)90,4784
Polymers89,6712
Non-polymers8072
Water20,6091144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-24 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.380, 97.853, 69.690
Angle α, β, γ (deg.)90.00, 116.27, 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.) Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1) (fungus)
Gene: FGM3, FGRAMPH1_01T20965 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C3YKE0, Transferases
#2: Chemical ChemComp-EQJ / (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine


Mass: 403.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1144 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M PCTP and 25% w/v PEG 1500, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.9→62.49 Å / Num. obs: 65508 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.06 / Rrim(I) all: 0.151 / Χ2: 1 / Net I/σ(I): 11.8 / Num. measured all: 404345
Reflection shellResolution: 1.9→2 Å / % possible obs: 98.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.622 / Num. measured all: 42430 / Num. unique obs: 9473 / CC1/2: 0.797 / Rpim(I) all: 0.321 / Rrim(I) all: 0.704 / Χ2: 0.93 / Net I/σ(I) obs: 2.5

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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: 1.9→59.05 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1821 1979 3.02 %
Rwork0.1535 --
obs0.1544 65450 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→59.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6111 0 54 1144 7309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076281
X-RAY DIFFRACTIONf_angle_d0.8998564
X-RAY DIFFRACTIONf_dihedral_angle_d6.95863
X-RAY DIFFRACTIONf_chiral_restr0.057997
X-RAY DIFFRACTIONf_plane_restr0.0081098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.26031310.22464420X-RAY DIFFRACTION98
1.95-20.22051520.19554552X-RAY DIFFRACTION100
2-2.060.20881380.18384506X-RAY DIFFRACTION100
2.06-2.130.18921500.17224515X-RAY DIFFRACTION100
2.13-2.20.22691200.16094516X-RAY DIFFRACTION100
2.2-2.290.20951580.16334531X-RAY DIFFRACTION100
2.29-2.40.19011550.15474568X-RAY DIFFRACTION100
2.4-2.520.17831230.14554508X-RAY DIFFRACTION100
2.52-2.680.18621490.15124544X-RAY DIFFRACTION100
2.68-2.890.18191290.15044570X-RAY DIFFRACTION100
2.89-3.180.19221540.14884528X-RAY DIFFRACTION100
3.18-3.640.16811370.14044555X-RAY DIFFRACTION100
3.64-4.580.14021480.12654555X-RAY DIFFRACTION100
4.58-59.050.15551350.14864603X-RAY DIFFRACTION99

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