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- PDB-7wvs: The structure of FinI complex with SAM -

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Basic information

Entry
Database: PDB / ID: 7wvs
TitleThe structure of FinI complex with SAM
ComponentsMethyltransf_2 domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Complex / Diels-Alderase
Function / homology
Function and homology information


secondary metabolite biosynthetic process / O-methyltransferase activity / 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
S-ADENOSYLMETHIONINE / O-methyltransferase domain-containing protein
Similarity search - Component
Biological speciesAspergillus carbonarius ITEM 5010 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLu, J. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91856202 China
CitationJournal: To Be Published
Title: The structure of FinI complex with SAM
Authors: Lu, J. / Zhou, J.
History
DepositionFeb 11, 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)94,74048
Polymers90,8582
Non-polymers3,88246
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-92 kcal/mol
Surface area30580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.555, 108.760, 124.176
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
Components on special symmetry positions
IDModelComponents
11B-682-

HOH

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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 , 5 types, 300 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Lithium sulfate, 0.1 M MES pH 6, 20%(w/v)PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→28.81 Å / Num. obs: 42257 / % possible obs: 99 % / Redundancy: 13.3 % / Biso Wilson estimate: 30.79 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.081 / Rrim(I) all: 0.215 / Net I/σ(I): 8.1
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3082 / CC1/2: 0.904 / Rpim(I) all: 0.259 / Rrim(I) all: 0.691 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHENIX1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WUP

7wup


Resolution: 2.35→28.6 Å / SU ML: 0.2405 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.0752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 2103 4.98 %
Rwork0.1701 40084 -
obs0.1725 42187 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.14 Å2
Refinement stepCycle: LAST / Resolution: 2.35→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6114 0 246 254 6614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00666460
X-RAY DIFFRACTIONf_angle_d0.79838704
X-RAY DIFFRACTIONf_chiral_restr0.048980
X-RAY DIFFRACTIONf_plane_restr0.00471089
X-RAY DIFFRACTIONf_dihedral_angle_d16.7871923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.27011380.22627X-RAY DIFFRACTION99.96
2.4-2.460.24651250.19022656X-RAY DIFFRACTION100
2.46-2.530.24451300.18522670X-RAY DIFFRACTION100
2.53-2.610.25181380.18122600X-RAY DIFFRACTION99.96
2.61-2.690.25521560.18162624X-RAY DIFFRACTION99.96
2.69-2.790.24161410.16932645X-RAY DIFFRACTION100
2.79-2.90.23561510.17582627X-RAY DIFFRACTION100
2.9-3.030.23551210.16662678X-RAY DIFFRACTION100
3.03-3.190.23411350.17252675X-RAY DIFFRACTION100
3.19-3.390.21061560.16882639X-RAY DIFFRACTION100
3.39-3.650.22361310.16632688X-RAY DIFFRACTION100
3.65-4.020.1811590.15722678X-RAY DIFFRACTION100
4.02-4.590.18681250.14492717X-RAY DIFFRACTION100
4.59-5.780.21431320.17522730X-RAY DIFFRACTION100
5.78-28.60.20871650.18132830X-RAY DIFFRACTION99.14

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