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- PDB-8ffu: Structure of GntC, a PLP-dependent enzyme catalyzing L-enduracidi... -

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Basic information

Entry
Database: PDB / ID: 8ffu
TitleStructure of GntC, a PLP-dependent enzyme catalyzing L-enduracididine biosynthesis from (S)-4-hydroxy-L-arginine, with the substrate bound
Components(Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme) x 2
KeywordsBIOSYNTHETIC PROTEIN / PLP / GntC / cyclodehydration / (S)-4-hydroxy-L-arginine / guanitoxin / L-enduracididine / cyanobacterial blooms / biocatalysis / biosynthesis / cyanobacterium
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-XUR / Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Similarity search - Component
Biological speciesDolichospermum flos-aquae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsChen, P.Y.-T. / Moore, B.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R21-ES032056 United States
Citation
Journal: Acs Catalysis / Year: 2023
Title: Mechanistic and Structural Insights into a Divergent PLP-Dependent l-Enduracididine Cyclase from a Toxic Cyanobacterium.
Authors: Cordoza, J.L. / Chen, P.Y. / Blaustein, L.R. / Lima, S.T. / Fiore, M.F. / Chekan, J.R. / Moore, B.S. / McKinnie, S.M.K.
#1: Journal: Biorxiv / Year: 2023
Title: Mechanistic and structural insights into a divergent PLP-dependent L-enduracididine cyclase from a toxic cyanobacterium.
Authors: Cordoza, J.L. / Chen, P.Y. / Blaustein, L.R. / Lima, S.T. / Fiore, M.F. / Chekan, J.R. / Moore, B.S. / McKinnie, S.M.K.
History
DepositionDec 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
C: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
D: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,94210
Polymers167,0074
Non-polymers9366
Water2,936163
1
A: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9715
Polymers83,5032
Non-polymers4683
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
D: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9715
Polymers83,5032
Non-polymers4683
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.062, 158.489, 73.600
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme


Mass: 41637.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dolichospermum flos-aquae (bacteria) / Gene: K2F26_16465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8G0W655
#2: Protein Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme


Mass: 41865.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dolichospermum flos-aquae (bacteria) / Gene: K2F26_16465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8G0W655
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-XUR / (2S,4S)-5-carbamimidamido-4-hydroxy-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pentanoic acid (non-preferred name)


Mass: 419.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N5O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 24-27% (w/v) PEG 3350, 0.40-0.44 M MgCl2, 0.10 M Tris pH 8.5, 1 mM PLP, and 10 mM S-4-hydroxy-L-Arg

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→100 Å / Num. obs: 87584 / % possible obs: 98.6 % / Redundancy: 5.8 % / Rsym value: 0.094 / Net I/σ(I): 13.56
Reflection shellResolution: 2.04→2.16 Å / Num. unique obs: 14110 / CC1/2: 0.705 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8FFT

8fft


Resolution: 2.04→36.8 Å / Cross valid method: FREE R-VALUE / σ(F): 95.95 / Phase error: 24.4897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 4313 4.92 %
Rwork0.176 83270 -
obs0.1911 87583 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.12 Å2
Refinement stepCycle: LAST / Resolution: 2.04→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11319 0 60 163 11542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003711632
X-RAY DIFFRACTIONf_angle_d0.678815836
X-RAY DIFFRACTIONf_chiral_restr0.04831811
X-RAY DIFFRACTIONf_plane_restr0.00482089
X-RAY DIFFRACTIONf_dihedral_angle_d11.7014308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.070.30622110.27884096X-RAY DIFFRACTION93.56
2.07-2.110.27812220.26694191X-RAY DIFFRACTION94.39
2.11-2.150.30272260.25784138X-RAY DIFFRACTION93.41
2.15-2.20.27232100.25444165X-RAY DIFFRACTION93.87
2.2-2.240.28942170.24954172X-RAY DIFFRACTION93.96
2.24-2.30.26492080.24714117X-RAY DIFFRACTION92.81
2.3-2.350.27732120.24274096X-RAY DIFFRACTION93.2
2.35-2.420.26582050.23234183X-RAY DIFFRACTION94.62
2.42-2.490.25241910.23334208X-RAY DIFFRACTION95.12
2.49-2.570.26222020.22454245X-RAY DIFFRACTION94.52
2.57-2.660.28452360.22464141X-RAY DIFFRACTION93.5
2.66-2.770.2551970.21484125X-RAY DIFFRACTION93.64
2.77-2.890.27172130.20924118X-RAY DIFFRACTION92.15
2.89-3.050.20582360.19934166X-RAY DIFFRACTION94.06
3.05-3.240.25841920.19714245X-RAY DIFFRACTION95.05
3.24-3.490.2412070.18354165X-RAY DIFFRACTION94.29
3.49-3.840.22222240.17234104X-RAY DIFFRACTION92.16
3.84-4.390.16592070.14754224X-RAY DIFFRACTION94.71
4.39-5.530.17872540.14094136X-RAY DIFFRACTION92.71
5.53-36.80.16382190.15164259X-RAY DIFFRACTION94.31

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