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- PDB-7dmb: Crystal structure of trans-methyltransferase CalH complex with SAH -

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Basic information

Entry
Database: PDB / ID: 7dmb
TitleCrystal structure of trans-methyltransferase CalH complex with SAH
ComponentsPutative methyltransferase
KeywordsTRANSFERASE / methyltransferase / CalH / Calbistrin A Biosynthesis
Function / homology: / Methyltransferase type 12 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Putative methyltransferase
Function and homology information
Biological speciesEmericella variicolor (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsTao, H. / Mori, T. / Abe, I.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: One Polyketide Synthase, Two Distinct Products: Trans-Acting Enzyme-Controlled Product Divergence in Calbistrin Biosynthesis.
Authors: Tao, H. / Mori, T. / Wei, X. / Matsuda, Y. / Abe, I.
History
DepositionDec 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methyltransferase
B: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6574
Polymers86,8882
Non-polymers7692
Water9,026501
1
A: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8292
Polymers43,4441
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8292
Polymers43,4441
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.810, 60.594, 71.146
Angle α, β, γ (deg.)87.786, 88.340, 89.742
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Putative methyltransferase


Mass: 43444.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella variicolor (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A679DLY7
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.0, 20% PEG4000, 0.5 mM SAH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→46.99 Å / Num. obs: 39461 / % possible obs: 97 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.22 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.131 / Net I/σ(I): 5.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3199 / CC1/2: 0.717

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.18.2_3874refinement
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→46.99 Å / SU ML: 0.2505 / Cross valid method: FREE R-VALUE / σ(F): 1.83 / Phase error: 23.3194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2434 1984 5.03 %
Rwork0.1864 37454 -
obs0.1891 39438 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5702 0 52 501 6255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00755910
X-RAY DIFFRACTIONf_angle_d0.88298044
X-RAY DIFFRACTIONf_chiral_restr0.0499860
X-RAY DIFFRACTIONf_plane_restr0.00691046
X-RAY DIFFRACTIONf_dihedral_angle_d20.11812216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.29671440.22262630X-RAY DIFFRACTION96.42
2.15-2.210.27711450.20742652X-RAY DIFFRACTION96.28
2.21-2.280.27441290.19832658X-RAY DIFFRACTION96.57
2.28-2.350.28481590.19342668X-RAY DIFFRACTION96.58
2.35-2.430.2651450.18982662X-RAY DIFFRACTION96.99
2.43-2.530.24231470.19342710X-RAY DIFFRACTION97.18
2.53-2.650.26031370.19082689X-RAY DIFFRACTION97.35
2.65-2.790.26941440.1872702X-RAY DIFFRACTION97.17
2.79-2.960.26831390.18822671X-RAY DIFFRACTION97.3
2.96-3.190.24851420.18412683X-RAY DIFFRACTION97.11
3.19-3.510.22741400.17962669X-RAY DIFFRACTION96.83
3.51-4.020.21721340.17612687X-RAY DIFFRACTION97.54
4.02-5.060.1941430.15862688X-RAY DIFFRACTION96.89
5.06-46.990.22761360.20142685X-RAY DIFFRACTION97.08

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