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- PDB-9x51: Crystal structure of Fgm3 in complex with PLP and 4(S)-OH-L-Arg -

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Basic information

Entry
Database: PDB / ID: 9x51
TitleCrystal structure of Fgm3 in complex with PLP and 4(S)-OH-L-Arg
ComponentsAminotransferase-like protein FGM3
KeywordsBIOSYNTHETIC PROTEIN / PLP / Retro-aldol-like / Cbeta-Cgamma Bond Cleavage
Function / homology
Function and homology information


Transferases / transferase activity
Similarity search - Function
Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / (2S,4S)-4-hydroxy-L-arginine / Aminotransferase-like protein FGM3
Similarity search - Component
Biological speciesFusarium graminearum PH-1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 14, 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

Downloads & links

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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)90,91410
Polymers89,6712
Non-polymers1,2438
Water16,916939
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-28 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.310, 97.400, 69.790
Angle α, β, γ (deg.)90.00, 116.36, 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-WYK / (2S,4S)-4-hydroxy-L-arginine / (2S,4S)-2-azanyl-5-carbamimidamido-4-oxidanyl-pentanoic acid


Type: L-peptide linking / Mass: 190.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N4O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 7.5% w/v PEG 20000/7.5% v/v PEG 550 MME, 0.1 M Tris, 0.08 M Sodium formate, pH 7.5

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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: Dec 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.48→62.1 Å / Num. obs: 135791 / % possible obs: 98.5 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.037 / Rrim(I) all: 0.092 / Χ2: 0.93 / Net I/σ(I): 13.9 / Num. measured all: 803731
Reflection shellResolution: 1.48→1.52 Å / % possible obs: 93.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.938 / Num. measured all: 37329 / Num. unique obs: 9508 / CC1/2: 0.505 / Rpim(I) all: 0.54 / Rrim(I) all: 1.091 / Χ2: 0.79 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→59.09 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1742 6531 4.8 %
Rwork0.1558 --
obs0.1567 135688 98.38 %
Refinement stepCycle: LAST / Resolution: 1.48→59.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6152 0 80 939 7171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066384
X-RAY DIFFRACTIONf_angle_d0.918703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.30492010.27773952X-RAY DIFFRACTION91
1.5-1.510.31212210.26274127X-RAY DIFFRACTION95
1.51-1.530.26762370.23884197X-RAY DIFFRACTION96
1.53-1.550.25562150.22784200X-RAY DIFFRACTION97
1.55-1.570.23241930.19964294X-RAY DIFFRACTION97
1.57-1.590.22321930.19214229X-RAY DIFFRACTION97
1.59-1.620.21161910.18544318X-RAY DIFFRACTION98
1.62-1.640.21832060.17894292X-RAY DIFFRACTION99
1.64-1.670.19832440.17554283X-RAY DIFFRACTION99
1.67-1.690.18911790.17254343X-RAY DIFFRACTION99
1.69-1.720.19232180.16584312X-RAY DIFFRACTION99
1.72-1.750.1852530.16524278X-RAY DIFFRACTION99
1.75-1.790.20251930.17154387X-RAY DIFFRACTION99
1.79-1.820.19092390.17034281X-RAY DIFFRACTION99
1.82-1.860.18672150.15694315X-RAY DIFFRACTION99
1.86-1.910.17672610.15754296X-RAY DIFFRACTION99
1.91-1.960.18822010.1524345X-RAY DIFFRACTION99
1.96-2.010.16451940.15334342X-RAY DIFFRACTION99
2.01-2.070.16231770.15564412X-RAY DIFFRACTION99
2.07-2.130.18332140.15614323X-RAY DIFFRACTION99
2.13-2.210.16252190.1554367X-RAY DIFFRACTION99
2.21-2.30.16592740.15044302X-RAY DIFFRACTION99
2.3-2.40.18762520.15474303X-RAY DIFFRACTION99
2.4-2.530.17532690.15084288X-RAY DIFFRACTION99
2.53-2.690.16282010.15484415X-RAY DIFFRACTION100
2.69-2.90.1632050.14864384X-RAY DIFFRACTION100
2.9-3.190.17812130.14944387X-RAY DIFFRACTION100
3.19-3.650.15062130.13714399X-RAY DIFFRACTION100
3.65-4.60.13532360.12674386X-RAY DIFFRACTION99
4.6-59.090.15721920.15114413X-RAY DIFFRACTION98

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