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- PDB-8gyh: Crystal structure of Fic25 (apo form) from Streptomyces ficellus -

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Basic information

Entry
Database: PDB / ID: 8gyh
TitleCrystal structure of Fic25 (apo form) from Streptomyces ficellus
ComponentsDegT/DnrJ/EryC1/StrS family aminotransferase
KeywordsBIOSYNTHETIC PROTEIN / Sugar aminotransferase / Biosynthetic enzyme / DADH
Function / homology
Function and homology information


dTDP-4-amino-4,6-dideoxygalactose transaminase activity / polysaccharide biosynthetic process / antibiotic biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
IMIDAZOLE / DegT/DnrJ/EryC1/StrS family aminotransferase
Similarity search - Component
Biological speciesStreptomyces ficellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKurosawa, S. / Yoshida, A. / Tomita, T. / Nishiyama, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24228001 Japan
Japan Society for the Promotion of Science (JSPS)17H06168 Japan
Japan Society for the Promotion of Science (JSPS)22H00355 Japan
Japan Science and TechnologyJPMJSP2108 Japan
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis.
Authors: Kurosawa, S. / Okamura, H. / Yoshida, A. / Tomita, T. / Sone, Y. / Hasebe, F. / Shinada, T. / Takikawa, H. / Kosono, S. / Nishiyama, M.
History
DepositionSep 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DegT/DnrJ/EryC1/StrS family aminotransferase
A: DegT/DnrJ/EryC1/StrS family aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,46811
Polymers93,8242
Non-polymers6459
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The interface area was 2,313 square angstrom as calculated by PISA.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-8 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.658, 201.658, 56.992
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DegT/DnrJ/EryC1/StrS family aminotransferase / Glutamine--scyllo-inositol transaminase / Fic25


Mass: 46911.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ficellus (bacteria) / Gene: EIZ62_06105 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W5T2G9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1.0 M Sodium citrate, 0.1 M Imidazole, pH8.0

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.484 Å / Num. obs: 122992 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Net I/σ(I): 18.9
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.94 / Num. unique obs: 6059 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model constructed by AlphaFold2 from the primary amino acid sequence of Fic25

Resolution: 1.8→48.48 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.223 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 6325 5.1 %RANDOM
Rwork0.171 ---
obs0.172 116639 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.56 Å2 / Biso mean: 21.536 Å2 / Biso min: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å2-0 Å2
3----2.35 Å2
Refinement stepCycle: final / Resolution: 1.8→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6299 0 46 745 7090
Biso mean--32.05 31.21 -
Num. residues----838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0126654
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166044
X-RAY DIFFRACTIONr_angle_refined_deg0.9321.6489071
X-RAY DIFFRACTIONr_angle_other_deg0.3221.56414019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.485570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1910972
X-RAY DIFFRACTIONr_chiral_restr0.0450.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021406
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 454 -
Rwork0.257 8567 -
all-9021 -
obs--99.91 %

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