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- PDB-5bp9: Crystal structure of SAM-dependent methyltransferase from Bactero... -

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Basic information

Entry
Database: PDB / ID: 5bp9
TitleCrystal structure of SAM-dependent methyltransferase from Bacteroides fragilis in complex with S-Adenosyl-L-homocysteine
ComponentsPutative methyltransferase protein
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homologyMethyltransferase domain / Methyltransferase type 11 / Methyltransferase domain / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Chem-ETE / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsGasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Cymborowski, M.T. / Mason, D.V. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: to be published
Title: Crystal structure of SAM-dependent methyltransferase fromBacteroides fragilis in complex with S-Adenosyl-L-homocysteine
Authors: Gasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Cymborowski, M.T. / Mason, D. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methyltransferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0904
Polymers32,3041
Non-polymers7873
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.732, 70.660, 78.743
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative methyltransferase protein


Mass: 32303.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein was incubated with TEV before crystallization.
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / DSM 2151 / JCM 11019 / NCTC 9343 / Gene: BF9343_1312 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q5LFK0
#2: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 31.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the TOP96 condition #29 (0.2 M Ammonium sulfate, 0.1 ...Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the TOP96 condition #29 (0.2 M Ammonium sulfate, 0.1 M Sodium Cacodylate:HCl pH 6.5, 30% (w/v) PEG 8000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 3 hours
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 38281 / Num. obs: 37846 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.03 / Rrim(I) all: 0.069 / Rsym value: 0.062 / Χ2: 1.824 / Net I/av σ(I): 33.435 / Net I/σ(I): 11.3 / Num. measured all: 187562
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.534.40.6921.918070.6770.3620.7840.78698
1.53-1.554.70.56518610.8160.280.6320.79797.7
1.55-1.5850.48518490.8730.2350.5410.78198.2
1.58-1.6250.43118450.8860.210.480.85397.9
1.62-1.6550.35818600.9210.1740.3990.86598.6
1.65-1.6950.30718600.9430.1480.3410.89798.6
1.69-1.7350.25918530.960.1250.2880.94198.8
1.73-1.7850.20918860.9720.1010.2330.99798.8
1.78-1.8350.1718740.9790.0830.191.07998.7
1.83-1.895.10.14618800.9830.0710.1631.17699.2
1.89-1.965.10.11418780.9890.0550.1271.33199.4
1.96-2.045.10.09318840.9930.0450.1041.49899.2
2.04-2.135.10.08118900.9950.0390.0911.65499.4
2.13-2.245.10.0719090.9960.0340.0781.84499.6
2.24-2.385.10.06719020.9960.0320.0752.18199.6
2.38-2.5650.06619200.9960.0320.0732.73499.6
2.56-2.8250.05619380.9960.0280.0632.93399.7
2.82-3.234.90.04919440.9980.0240.0543.63699.7
3.23-4.074.90.03919580.9990.0190.0443.60799.3
4.07-504.60.0420480.9980.020.0455.597.4

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000phasing
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1796 / WRfactor Rwork: 0.1319 / FOM work R set: 0.8908 / SU B: 2.499 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0747 / SU Rfree: 0.0699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.07 / SU Rfree Cruickshank DPI: 0.0699 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 1836 4.9 %RANDOM
Rwork0.1318 ---
obs0.1341 35821 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.52 Å2 / Biso mean: 22.973 Å2 / Biso min: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.4 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 53 338 2244
Biso mean--41.64 37.3 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192029
X-RAY DIFFRACTIONr_bond_other_d0.0020.021928
X-RAY DIFFRACTIONr_angle_refined_deg1.5622.0222745
X-RAY DIFFRACTIONr_angle_other_deg1.08534445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02723.91897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55215310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6051516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022283
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02463
X-RAY DIFFRACTIONr_mcbond_it3.1051.827976
X-RAY DIFFRACTIONr_mcbond_other3.0531.821975
X-RAY DIFFRACTIONr_mcangle_it3.2772.7151220
X-RAY DIFFRACTIONr_rigid_bond_restr7.22531976
X-RAY DIFFRACTIONr_sphericity_bonded16.1330.11929
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 134 -
Rwork0.226 2583 -
all-2717 -
obs--97.73 %

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