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- PDB-7wuy: The crystal structure of FinI in complex with SAM and fischerin -

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Basic information

Entry
Database: PDB / ID: 7wuy
TitleThe crystal structure of FinI in complex with SAM and fischerin
ComponentsMethyltransf_2 domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Complex
Function / homology
Function and homology information


: / : / O-methyltransferase activity / secondary metabolite biosynthetic process / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-76N / DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / O-methyltransferase domain-containing protein
Similarity search - Component
Biological speciesAspergillus carbonarius ITEM 5010 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsZhou, J. / Lu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91856202 China
CitationJournal: To Be Published
Title: The crystal structure of FinI in complex with SAM and fischerin
Authors: Zhou, J. / Lu, J.
History
DepositionFeb 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
A: Methyltransf_2 domain-containing protein
B: Methyltransf_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,50251
Polymers90,8582
Non-polymers4,64449
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18450 Å2
ΔGint-30 kcal/mol
Surface area29740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.954, 108.295, 122.771
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methyltransf_2 domain-containing protein


Mass: 45429.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus carbonarius ITEM 5010 (mold)
Strain: ITEM 5010 / Gene: ASPCADRAFT_492 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1R3S1W7

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Non-polymers , 8 types, 530 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-76N / 3-[[(1~{S},2~{R},4~{a}~{S},8~{a}~{S})-2-methyl-1,2,4~{a},5,6,7,8,8~{a}-octahydronaphthalen-1-yl]carbonyl]-5-[(1~{S},2~{R},5~{S},6~{S})-2,5-bis(oxidanyl)-7-oxabicyclo[4.1.0]heptan-2-yl]-4-oxidanyl-1~{H}-pyridin-2-one


Mass: 415.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29NO6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M Ammonium sulfate, 0.1 M HEPES pH 7.0, 20%(w/v)PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.84→43.48 Å / Num. obs: 83669 / % possible obs: 98.6 % / Redundancy: 13.3 % / Biso Wilson estimate: 27.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.033 / Rrim(I) all: 0.088 / Net I/σ(I): 21.5
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.283 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4473 / CC1/2: 0.734 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WUP

7wup


Resolution: 1.84→40.61 Å / SU ML: 0.1943 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 4142 4.95 %
Rwork0.1699 79467 -
obs0.1719 83609 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.71 Å2
Refinement stepCycle: LAST / Resolution: 1.84→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 303 481 6906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01586544
X-RAY DIFFRACTIONf_angle_d1.30198811
X-RAY DIFFRACTIONf_chiral_restr0.0888991
X-RAY DIFFRACTIONf_plane_restr0.00911098
X-RAY DIFFRACTIONf_dihedral_angle_d11.1808963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.860.31941390.28382593X-RAY DIFFRACTION97.26
1.86-1.880.26631400.25142568X-RAY DIFFRACTION97.83
1.88-1.910.28151460.24422605X-RAY DIFFRACTION97.48
1.91-1.930.29791350.23052582X-RAY DIFFRACTION97.73
1.93-1.960.25851550.22792572X-RAY DIFFRACTION97.6
1.96-1.980.27021340.21452604X-RAY DIFFRACTION97.72
1.98-2.010.25161430.2052612X-RAY DIFFRACTION97.76
2.01-2.040.25341360.212614X-RAY DIFFRACTION98
2.04-2.070.27311470.1982595X-RAY DIFFRACTION97.55
2.07-2.110.23931280.1952616X-RAY DIFFRACTION98.6
2.11-2.140.22771410.18012586X-RAY DIFFRACTION97.18
2.14-2.180.24511480.17962612X-RAY DIFFRACTION98.92
2.18-2.220.23121350.17932606X-RAY DIFFRACTION97.61
2.22-2.270.22691550.17242626X-RAY DIFFRACTION98.16
2.27-2.320.20481510.17412605X-RAY DIFFRACTION98.75
2.32-2.370.2411250.16862641X-RAY DIFFRACTION97.84
2.37-2.430.20441130.16732649X-RAY DIFFRACTION98.05
2.43-2.50.21511210.16942671X-RAY DIFFRACTION99.11
2.5-2.570.19081330.1612671X-RAY DIFFRACTION98.87
2.57-2.650.22651370.172636X-RAY DIFFRACTION98.51
2.65-2.750.21771290.16282663X-RAY DIFFRACTION98.55
2.75-2.860.2591040.17272701X-RAY DIFFRACTION98.7
2.86-2.990.21391440.17082668X-RAY DIFFRACTION98.94
2.99-3.150.19541470.17462671X-RAY DIFFRACTION99.02
3.15-3.340.20791600.17132654X-RAY DIFFRACTION98.77
3.34-3.60.19991360.15882722X-RAY DIFFRACTION99.48
3.6-3.960.18441510.15412696X-RAY DIFFRACTION99.23
3.96-4.540.16551330.13672753X-RAY DIFFRACTION99.41
4.54-5.710.19551420.15872774X-RAY DIFFRACTION99.45
5.71-40.610.19111340.16482901X-RAY DIFFRACTION99.12

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