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- PDB-6uk5: Structure of SAM bound CalS10, an amino pentose methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 6uk5
TitleStructure of SAM bound CalS10, an amino pentose methyltransferase from Micromonospora echinaspora involved in calicheamicin biosynthesis
ComponentsCalS10
KeywordsTRANSFERASE / methyltransferase / natural product / calicheamicin biosynthesis
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / ACETATE ION / DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / CalS10
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsAlvarado, S.K. / Miller, M.D. / Xu, W. / Wang, Z. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115261 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098248 United States
National Science Foundation (NSF, United States)STC 1231306 United States
CitationJournal: To Be Published
Title: Structure of SAM bound CalS10, an amino pentose methyltransferase from Micromonospora echinaspora involved in calicheamicin biosynthesis
Authors: Alvarado, S.K. / Miller, M.D. / Xu, W. / Wang, Z. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionOct 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: CalS10
B: CalS10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,86610
Polymers57,2632
Non-polymers1,6048
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography supports the assignment of a dimer as the biological unit.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-14 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.290, 133.290, 81.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 9 through 236 or resid 485 through 901))A9 - 236
121(chain 'A' and (resid 9 through 236 or resid 485 through 901))A485
131(chain 'A' and (resid 9 through 236 or resid 485 through 901))A701
141(chain 'A' and (resid 9 through 236 or resid 485 through 901))A901
251(chain 'B' and (resid 9 through 236 or resid 585 through 1001))B9 - 236
261(chain 'B' and (resid 9 through 236 or resid 585 through 1001))B585
271(chain 'B' and (resid 9 through 236 or resid 585 through 1001))B801
281(chain 'B' and (resid 9 through 236 or resid 585 through 1001))B1001

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CalS10


Mass: 28631.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calS10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8KNF4

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Non-polymers , 5 types, 34 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M sodium citrate pH5.5, 24% PEG 400, 0.28M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2018 / Details: Bimorph K-B pair
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.6→66.71 Å / Num. obs: 25648 / % possible obs: 100 % / Redundancy: 17.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.036 / Rrim(I) all: 0.153 / Net I/σ(I): 12.2 / Num. measured all: 459637 / Scaling rejects: 2080
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.6718.31.1773490019030.6420.2811.2112.7100
11.63-66.7115.70.04348263070.9990.0110.04527.699.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.19 Å66.72 Å
Translation3.19 Å66.72 Å

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Processing

Software
NameVersionClassificationNB
DIALS1.8.2-g5331de77-releasedata reduction
Aimless0.6.2data scaling
PHASER2.8.0phasing
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bxo

3bxo


Resolution: 2.6→47.15 Å / SU ML: 0.3649 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 28.3666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2507 1339 5.23 %
Rwork0.2309 24278 -
obs0.2319 25617 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 108 26 3820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343878
X-RAY DIFFRACTIONf_angle_d0.76825240
X-RAY DIFFRACTIONf_chiral_restr0.0474560
X-RAY DIFFRACTIONf_plane_restr0.0034706
X-RAY DIFFRACTIONf_dihedral_angle_d15.15372255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.38251450.34162384X-RAY DIFFRACTION99.02
2.69-2.80.33441140.33012420X-RAY DIFFRACTION100
2.8-2.930.3251300.32172430X-RAY DIFFRACTION100
2.93-3.080.32211500.3022390X-RAY DIFFRACTION99.96
3.08-3.270.32941400.30352430X-RAY DIFFRACTION100
3.27-3.530.29311280.27822422X-RAY DIFFRACTION99.96
3.53-3.880.27641270.25162436X-RAY DIFFRACTION100
3.88-4.440.22151000.20492461X-RAY DIFFRACTION100
4.44-5.590.19841430.17342449X-RAY DIFFRACTION100
5.59-47.150.20171620.17762456X-RAY DIFFRACTION99.7

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