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- PDB-9x5b: Crystal structure of Fgm3 in complex with PLP and L-Arg -

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Basic information

Entry
Database: PDB / ID: 9x5b
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 / ARGININE / Aminotransferase-like protein FGM3
Function and homology information
Biological speciesFusarium graminearum PH-1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 13, 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)91,1388
Polymers90,1272
Non-polymers1,0116
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-18 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.550, 97.779, 69.763
Angle α, β, γ (deg.)90.00, 116.10, 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: 45063.562 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-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium HEPES, 25% w/v PEG 3350, pH 7.5

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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: 2.18→62.65 Å / Num. obs: 43839 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.139 / Rrim(I) all: 0.252 / Χ2: 1.03 / Net I/σ(I): 9
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.804 / Num. unique obs: 6350 / CC1/2: 0.733 / Rpim(I) all: 0.558 / Rrim(I) all: 0.982 / Χ2: 0.97

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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: 2.18→62.65 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2289 1956 4.47 %
Rwork0.1697 --
obs0.1723 43764 99.93 %
Refinement stepCycle: LAST / Resolution: 2.18→62.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 66 540 6732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086318
X-RAY DIFFRACTIONf_angle_d0.8668610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.230.31961380.23372976X-RAY DIFFRACTION100
2.23-2.290.27651430.20692924X-RAY DIFFRACTION100
2.29-2.360.30091320.19473022X-RAY DIFFRACTION100
2.36-2.440.23731480.18572940X-RAY DIFFRACTION100
2.44-2.520.251500.16752978X-RAY DIFFRACTION100
2.52-2.630.24931300.17022997X-RAY DIFFRACTION100
2.63-2.750.2071450.16272999X-RAY DIFFRACTION100
2.75-2.890.2141310.16372984X-RAY DIFFRACTION100
2.89-3.070.24861300.16513006X-RAY DIFFRACTION100
3.07-3.310.22251330.16352983X-RAY DIFFRACTION100
3.31-3.640.20851560.1552963X-RAY DIFFRACTION100
3.64-4.170.19281330.14293000X-RAY DIFFRACTION100
4.17-5.250.20681570.15523000X-RAY DIFFRACTION100
5.25-62.650.22641300.18973036X-RAY DIFFRACTION99

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