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- PDB-9x4u: Crystal structure of Fgm3 in complex with PLP -

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Basic information

Entry
Database: PDB / ID: 9x4u
TitleCrystal structure of Fgm3 in complex with PLP
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 / Aminotransferase-like protein FGM3
Function and homology information
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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
C: Aminotransferase-like protein FGM3
D: Aminotransferase-like protein FGM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,3468
Polymers180,2544
Non-polymers924
Water39,1652174
1
A: Aminotransferase-like protein FGM3
B: Aminotransferase-like protein FGM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1734
Polymers90,1272
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-44 kcal/mol
Surface area26770 Å2
MethodPISA
2
C: Aminotransferase-like protein FGM3
D: Aminotransferase-like protein FGM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1734
Polymers90,1272
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-45 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.804, 97.693, 124.678
Angle α, β, γ (deg.)90.00, 93.72, 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.: 4
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2174 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.03M Sodium fluoride, 0.03M Sodium bromide, 0.03M Sodium iodide, 0.1 M Sodium HEPES, 0.1 M MOPS (acid), 20% v/v PEG 500 MME, 10% w/v PEG 20000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.67→124.42 Å / Num. obs: 191763 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.7
Reflection shellResolution: 1.67→1.71 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 13205 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHASERphasing
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→21.9 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2033 9445 4.94 %
Rwork0.1781 --
obs0.1793 191052 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12320 0 64 2174 14558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712682
X-RAY DIFFRACTIONf_angle_d0.90517306
X-RAY DIFFRACTIONf_dihedral_angle_d8.1721720
X-RAY DIFFRACTIONf_chiral_restr0.0592012
X-RAY DIFFRACTIONf_plane_restr0.0092206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.25392610.21385472X-RAY DIFFRACTION89
1.69-1.710.23222500.20435789X-RAY DIFFRACTION94
1.71-1.730.23342930.20115966X-RAY DIFFRACTION99
1.73-1.750.24433290.1956064X-RAY DIFFRACTION99
1.75-1.770.23113360.19186043X-RAY DIFFRACTION99
1.77-1.80.20193230.19376033X-RAY DIFFRACTION99
1.8-1.820.22353310.19196019X-RAY DIFFRACTION99
1.82-1.850.20983570.18056057X-RAY DIFFRACTION99
1.85-1.880.22023360.19256074X-RAY DIFFRACTION99
1.88-1.910.27193280.22216006X-RAY DIFFRACTION99
1.91-1.940.26653330.22946027X-RAY DIFFRACTION99
1.94-1.980.2313620.19266051X-RAY DIFFRACTION100
1.98-2.020.19953200.18616041X-RAY DIFFRACTION100
2.02-2.060.25413000.19826123X-RAY DIFFRACTION100
2.06-2.10.2462900.21456081X-RAY DIFFRACTION99
2.1-2.150.20183330.17746044X-RAY DIFFRACTION100
2.15-2.210.22153360.17426101X-RAY DIFFRACTION100
2.21-2.270.22353210.20286065X-RAY DIFFRACTION99
2.27-2.330.22513190.17196092X-RAY DIFFRACTION100
2.33-2.410.17942980.16756133X-RAY DIFFRACTION100
2.41-2.490.19842870.16756159X-RAY DIFFRACTION100
2.49-2.590.19063080.1666106X-RAY DIFFRACTION100
2.59-2.710.20343310.16836110X-RAY DIFFRACTION100
2.71-2.850.19773290.16596105X-RAY DIFFRACTION100
2.85-3.030.19153470.16586114X-RAY DIFFRACTION100
3.03-3.270.19563020.16696143X-RAY DIFFRACTION100
3.27-3.590.17163160.16496127X-RAY DIFFRACTION100
3.59-4.110.16852870.16286211X-RAY DIFFRACTION100
4.11-5.170.15722880.15226199X-RAY DIFFRACTION100
5.17-21.90.17412940.16936052X-RAY DIFFRACTION96

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