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- PDB-6kjg: Crystal structure of PsoF -

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Basic information

Entry
Database: PDB / ID: 6kjg
TitleCrystal structure of PsoF
ComponentsDual-functional monooxygenase/methyltransferase psoF
KeywordsOXIDOREDUCTASE / metyltransferase
Function / homology
Function and homology information


fumagillin biosynthetic process / N,N-dimethylaniline monooxygenase activity / Oxidoreductases / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / monooxygenase activity / NADP binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / Methyltransferase type 12 / Methyltransferase domain / FAD/NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Dual-functional monooxygenase/methyltransferase psoF
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHara, K. / Hashimoto, H. / Matsushita, T. / Tsunematsu, Y. / Watanabe, K.
CitationJournal: Biochemistry / Year: 2019
Title: Functional and Structural Analyses oftrans C-Methyltransferase in Fungal Polyketide Biosynthesis.
Authors: Kishimoto, S. / Tsunematsu, Y. / Matsushita, T. / Hara, K. / Hashimoto, H. / Tang, Y. / Watanabe, K.
History
DepositionJul 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Dual-functional monooxygenase/methyltransferase psoF
B: Dual-functional monooxygenase/methyltransferase psoF
C: Dual-functional monooxygenase/methyltransferase psoF


Theoretical massNumber of molelcules
Total (without water)125,1963
Polymers125,1963
Non-polymers00
Water8,773487
1
A: Dual-functional monooxygenase/methyltransferase psoF


Theoretical massNumber of molelcules
Total (without water)41,7321
Polymers41,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual-functional monooxygenase/methyltransferase psoF


Theoretical massNumber of molelcules
Total (without water)41,7321
Polymers41,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual-functional monooxygenase/methyltransferase psoF


Theoretical massNumber of molelcules
Total (without water)41,7321
Polymers41,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.238, 44.102, 142.616
Angle α, β, γ (deg.)90.00, 93.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1048-

HOH

21C-1067-

HOH

31C-1157-

HOH

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Components

#1: Protein Dual-functional monooxygenase/methyltransferase psoF / Pseurotin biosynthesis protein F


Mass: 41732.039 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: psoF, AFUA_8G00440 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WAZ0, Oxidoreductases, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium fluoride, bis-tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. obs: 80787 / % possible obs: 98.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.87
Reflection shellResolution: 1.99→2.09 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 12540 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5THY

5thy


Resolution: 1.99→19.8 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2296 --
Rwork0.1966 --
all0.2296 --
obs0.1982 80772 98.5 %
Refinement stepCycle: LAST / Resolution: 1.99→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8126 0 0 487 8613

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