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- PDB-8dl5: Crystal structure of PLP-dependent Mannich cyclase LolT -

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Basic information

Entry
Database: PDB / ID: 8dl5
TitleCrystal structure of PLP-dependent Mannich cyclase LolT
ComponentsAminotransferase, class V/Cysteine desulfurase
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent C-C bond forming Cyclase
Function / homologyAminotransferase class V domain / Aminotransferase class-V / transaminase activity / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Aminotransferase, class V/Cysteine desulfurase
Function and homology information
Biological speciesPenicillium expansum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGao, J. / Hai, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Catal / Year: 2023
Title: A pyridoxal 5'-phosphate-dependent Mannich cyclase.
Authors: Gao, J. / Liu, S. / Zhou, C. / Lara, D. / Zou, Y. / Hai, Y.
History
DepositionJul 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase, class V/Cysteine desulfurase
B: Aminotransferase, class V/Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2513
Polymers111,1582
Non-polymers921
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-41 kcal/mol
Surface area29180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.837, 77.837, 298.842
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein Aminotransferase, class V/Cysteine desulfurase / PLP-dependent Mannich cyclase LolT


Mass: 55579.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium expansum (fungus) / Gene: PEX2_110450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A2J6G6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate, pH 5.18, 14% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 62480 / % possible obs: 100 % / Redundancy: 18.8 % / Biso Wilson estimate: 37.92 Å2 / CC1/2: 0.974 / CC star: 0.993 / Rpim(I) all: 0.042 / Net I/σ(I): 27.22
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 16.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3034 / CC1/2: 0.713 / CC star: 0.912 / Rpim(I) all: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2 predicted model

Resolution: 2.1→37.66 Å / SU ML: 0.2878 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2608 3144 5.03 %
Rwork0.233 59335 -
obs0.2344 62479 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 6 184 6655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456630
X-RAY DIFFRACTIONf_angle_d0.86569015
X-RAY DIFFRACTIONf_chiral_restr0.05061004
X-RAY DIFFRACTIONf_plane_restr0.0061155
X-RAY DIFFRACTIONf_dihedral_angle_d14.6824895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.37361380.27822567X-RAY DIFFRACTION98.22
2.13-2.170.32341540.27012669X-RAY DIFFRACTION100
2.17-2.210.34071280.28712662X-RAY DIFFRACTION100
2.21-2.250.34391480.27592643X-RAY DIFFRACTION100
2.25-2.290.28391570.27572669X-RAY DIFFRACTION100
2.29-2.340.32351120.26562658X-RAY DIFFRACTION99.96
2.34-2.390.31081290.25242647X-RAY DIFFRACTION99.96
2.39-2.440.30681540.25872694X-RAY DIFFRACTION100
2.44-2.50.2881440.23942681X-RAY DIFFRACTION100
2.5-2.570.26221340.24752660X-RAY DIFFRACTION100
2.57-2.650.34211570.2572659X-RAY DIFFRACTION100
2.65-2.730.28391410.24562663X-RAY DIFFRACTION100
2.73-2.830.29781500.24142696X-RAY DIFFRACTION100
2.83-2.940.3091270.25492693X-RAY DIFFRACTION99.96
2.94-3.080.23451280.22842725X-RAY DIFFRACTION100
3.08-3.240.28341360.24282720X-RAY DIFFRACTION100
3.24-3.440.291500.23672669X-RAY DIFFRACTION99.96
3.44-3.710.22431520.22822741X-RAY DIFFRACTION100
3.71-4.080.22881460.20412745X-RAY DIFFRACTION99.9
4.08-4.670.22031550.19752723X-RAY DIFFRACTION99.9
4.67-5.880.22171680.2172775X-RAY DIFFRACTION99.97
5.88-37.660.25321360.23382976X-RAY DIFFRACTION99.49

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