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- PDB-5bsz: X-ray structure of the sugar N-methyltransferase KedS8 from Strep... -

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Basic information

Entry
Database: PDB / ID: 5bsz
TitleX-ray structure of the sugar N-methyltransferase KedS8 from Streptoalloteichus sp ATCC 53650
ComponentsN-methyltransferase
KeywordsTRANSFERASE / N-methyltransferase kedarcidin trideoxysugar S-adenosylmethionine
Function / homology: / Methyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / THYMIDINE / N-methyltransferase
Function and homology information
Biological speciesStreptoalloteichus sp. ATCC 53650 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThoden, J.B. / Delvaux, N.A. / Holden, H.M.
CitationJournal: Protein Sci. / Year: 2015
Title: Molecular architecture of KedS8, a sugar N-methyltransferase from Streptoalloteichus sp. ATCC 53650.
Authors: Delvaux, N.A. / Thoden, J.B. / Holden, H.M.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9897
Polymers27,1151
Non-polymers8756
Water2,918162
1
A: N-methyltransferase
hetero molecules

A: N-methyltransferase
hetero molecules

A: N-methyltransferase
hetero molecules

A: N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,95828
Polymers108,4584
Non-polymers3,50024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area17270 Å2
ΔGint-12 kcal/mol
Surface area37500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.254, 81.004, 126.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

21A-558-

HOH

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Components

#1: Protein N-methyltransferase


Mass: 27114.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus sp. ATCC 53650 (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): rosetta2(DE3) / References: UniProt: K4P132
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 28-33% MPD, 2.5 mM SAH, 100 mM MOPS / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 21803 / Num. obs: 21803 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.2 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bxo

3bxo


Resolution: 2→28.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.117 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22577 1114 5.1 %RANDOM
Rwork0.1678 ---
obs0.17062 20689 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.478 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--0.31 Å20 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 2→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 59 162 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192013
X-RAY DIFFRACTIONr_bond_other_d00.021892
X-RAY DIFFRACTIONr_angle_refined_deg1.951.9642736
X-RAY DIFFRACTIONr_angle_other_deg0.84134316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2165254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4721.36895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89315290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4921525
X-RAY DIFFRACTIONr_chiral_restr0.1250.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212298
X-RAY DIFFRACTIONr_gen_planes_other00.02499
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 85 -
Rwork0.208 1421 -
obs--91.49 %

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