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- PDB-7ww0: The crystal structure of FinI complex with SAH -

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Basic information

Entry
Database: PDB / ID: 7ww0
TitleThe crystal structure of FinI complex with SAH
ComponentsMethyltransf_2 domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Complex / Diels-Alderase
Function / homology
Function and homology information


O-methyltransferase activity / secondary metabolite biosynthetic process / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase domain-containing protein
Similarity search - Component
Biological speciesAspergillus carbonarius ITEM 5010 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 complex with SAH
Authors: Zhou, J. / Lu, J.
History
DepositionFeb 12, 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

Downloads & links

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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)92,99519
Polymers90,8582
Non-polymers2,13717
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-135 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.832, 110.062, 123.748
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
11A-1575-

HOH

21B-914-

HOH

31B-1105-

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 , 7 types, 580 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20%(w/v)PEG8000

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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: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→73.83 Å / Num. obs: 86691 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 32.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Net I/σ(I): 22
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4535 / CC1/2: 0.731 / Rpim(I) all: 0.498 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WVS

7wvs


Resolution: 1.85→63.4 Å / SU ML: 0.1976 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 4313 4.98 %
Rwork0.1759 82263 -
obs0.1775 86576 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.97 Å2
Refinement stepCycle: LAST / Resolution: 1.85→63.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 134 563 6819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01196412
X-RAY DIFFRACTIONf_angle_d1.08048700
X-RAY DIFFRACTIONf_chiral_restr0.0674984
X-RAY DIFFRACTIONf_plane_restr0.00711097
X-RAY DIFFRACTIONf_dihedral_angle_d18.9843913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.32891360.26232726X-RAY DIFFRACTION100
1.87-1.890.28121520.24342713X-RAY DIFFRACTION100
1.89-1.920.26691320.24212677X-RAY DIFFRACTION100
1.92-1.940.28181380.23562729X-RAY DIFFRACTION100
1.94-1.970.28011380.2282729X-RAY DIFFRACTION99.97
1.97-1.990.25221420.21722722X-RAY DIFFRACTION99.93
1.99-2.020.23081380.2132686X-RAY DIFFRACTION99.65
2.02-2.050.27361430.20942718X-RAY DIFFRACTION99.97
2.05-2.080.24841420.20542705X-RAY DIFFRACTION100
2.08-2.120.24551410.19892749X-RAY DIFFRACTION100
2.12-2.150.23021400.20262708X-RAY DIFFRACTION100
2.15-2.190.23221310.19562723X-RAY DIFFRACTION100
2.19-2.240.2561700.18882718X-RAY DIFFRACTION100
2.24-2.280.25241270.19162698X-RAY DIFFRACTION99.96
2.28-2.330.21971410.19062768X-RAY DIFFRACTION99.79
2.33-2.390.26131380.18412722X-RAY DIFFRACTION100
2.39-2.440.22531360.18682743X-RAY DIFFRACTION100
2.44-2.510.22671540.18622708X-RAY DIFFRACTION100
2.51-2.580.20191380.18372746X-RAY DIFFRACTION100
2.58-2.670.2291740.19042712X-RAY DIFFRACTION99.93
2.67-2.760.20411690.19332711X-RAY DIFFRACTION99.76
2.76-2.870.22681380.18462749X-RAY DIFFRACTION100
2.87-30.20611440.18062755X-RAY DIFFRACTION100
3.01-3.160.22641460.19112757X-RAY DIFFRACTION100
3.16-3.360.18681490.18672772X-RAY DIFFRACTION100
3.36-3.620.20891380.16612759X-RAY DIFFRACTION99.79
3.62-3.990.18321380.15182795X-RAY DIFFRACTION99.97
3.99-4.560.14531490.13322803X-RAY DIFFRACTION100
4.56-5.750.18561490.15032844X-RAY DIFFRACTION99.93
5.75-63.40.18921420.1652918X-RAY DIFFRACTION97.76

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