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- PDB-7v6h: Crystal Structure of the SpnL -

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Basic information

Entry
Database: PDB / ID: 7v6h
TitleCrystal Structure of the SpnL
ComponentsCyclopropane fatty-acyl-phospholipid synthase-like methyltransferase
KeywordsTRANSFERASE / SpnL / Rauhut-Currier reaction / spinosyn A / Saccharopolyspora spinosa / BIOSYNTHETIC PROTEIN
Function / homology: / Methyltransferase type 11 / Methyltransferase domain / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase
Function and homology information
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.054 Å
AuthorsWu, H.-H. / Ko, T.-P. / Liu, H.-W. / Tsai, M.-D.
Funding support Taiwan, United States, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-109-TPP2 Taiwan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 040541 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Evidence for an Enzyme-Catalyzed Rauhut-Currier Reaction during the Biosynthesis of Spinosyn A.
Authors: Choi, S.H. / Jeon, B. / Kim, N. / Wu, H.H. / Ko, T.P. / Ruszczycky, M.W. / Isiorho, E.A. / Liu, Y.N. / Keatinge-Clay, A.T. / Tsai, M.D. / Liu, H.W.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase
B: Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2684
Polymers61,4992
Non-polymers7692
Water00
1
A: Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1342
Polymers30,7501
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1342
Polymers30,7501
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.351, 177.351, 116.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase


Mass: 30749.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: A8926_6440 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N3Y640
#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
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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.3 M sodium citrate, 100 mM Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 13408 / % possible obs: 99.7 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.5
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 8.9 / Num. unique obs: 644 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.054→46.347 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 617 4.62 %
Rwork0.2038 --
obs0.2062 13348 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.054→46.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4112 0 0 0 4112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d1.4835718
X-RAY DIFFRACTIONf_dihedral_angle_d8.972462
X-RAY DIFFRACTIONf_chiral_restr0.075634
X-RAY DIFFRACTIONf_plane_restr0.009750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.054-3.36110.38111700.30833085X-RAY DIFFRACTION98
3.3611-3.84730.27031140.24793194X-RAY DIFFRACTION99
3.8473-4.84640.24361600.20143183X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -38.1683 Å / Origin y: 22.934 Å / Origin z: -5.1144 Å
111213212223313233
T0.511 Å2-0.1686 Å20.058 Å2-0.7072 Å20.0489 Å2--0.6625 Å2
L1.2406 °20.0695 °20.7297 °2-0.6931 °2-0.3576 °2--3.3355 °2
S0.0119 Å °-0.4783 Å °-0.1214 Å °0.0784 Å °-0.1529 Å °-0.078 Å °0.0853 Å °0.2694 Å °0.1048 Å °
Refinement TLS groupSelection details: all

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