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Basic information

Entry
Database: PDB / ID: 5epe
TitleCrystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / SAM-dependent methyltransferase / PSI-Biology / S-Adenosyl-L-homocysteine / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


methyltransferase activity
Similarity search - Function
Predicted S-adenosyl-L-methionine dependent methyltransferase, YjhP-type / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesThiobacillus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsLaRowe, C. / Shabalin, I.G. / Kutner, J. / Handing, K.B. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Seidel, R. / Bonanno, J. / Almo, S.C. ...LaRowe, C. / Shabalin, I.G. / Kutner, J. / Handing, K.B. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Seidel, R. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: to be published
Title: Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine
Authors: LaRowe, C. / Shabalin, I.G. / Kutner, J. / Handing, K.B. / Minor, W.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Other
Revision 1.2Feb 24, 2016Group: Other
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.7Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8553
Polymers27,4471
Non-polymers4072
Water4,972276
1
A: SAM-dependent methyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)334,25636
Polymers329,36712
Non-polymers4,88924
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation16_555x,-y+1/2,-z+1/21
crystal symmetry operation18_555z,-x+1/2,-y+1/21
crystal symmetry operation23_555y,-z+1/2,-x+1/21
crystal symmetry operation27_555-x+1/2,y,-z+1/21
crystal symmetry operation32_555-z+1/2,x,-y+1/21
crystal symmetry operation34_555-y+1/2,z,-x+1/21
crystal symmetry operation38_555-x+1/2,-y+1/2,z1
crystal symmetry operation43_555-z+1/2,-x+1/2,y1
crystal symmetry operation48_555-y+1/2,-z+1/2,x1
Buried area34550 Å2
ΔGint-231 kcal/mol
Surface area104610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.536, 157.536, 157.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

21A-601-

HOH

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 27447.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus denitrificans (bacteria) / Strain: ATCC 25259 / Gene: Tbd_1076 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q3SJX0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5
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 MCSG II condition #56 (0.1M CHES pH=9.5, 20%w/v ...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 MCSG II condition #56 (0.1M CHES pH=9.5, 20%w/v PEG 4K) 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

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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: 1.9→50 Å / Num. all: 25623 / Num. obs: 25623 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.031 / Rrim(I) all: 0.105 / Rsym value: 0.1 / Χ2: 0.943 / Net I/av σ(I): 26.273 / Net I/σ(I): 5.6 / Num. measured all: 292403
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
1.9-1.9310.70.914212540.810.2920.960.673100
1.93-1.9711.30.75412790.8660.2340.790.697100
1.97-2.0111.50.59512780.9180.1830.6230.716100
2.01-2.0511.40.55212410.9220.1710.5780.789100
2.05-2.0911.50.48112990.9380.1480.5030.772100
2.09-2.1411.50.37812640.9670.1160.3950.787100
2.14-2.1911.50.34512770.9690.1060.3610.799100
2.19-2.2511.50.28112700.9810.0870.2940.782100
2.25-2.3211.50.24512580.9830.0750.2560.82100
2.32-2.3911.40.23612920.9860.0730.2470.908100
2.39-2.4811.60.20212940.9880.0620.2110.868100
2.48-2.5811.60.17312490.990.0530.1810.907100
2.58-2.711.60.14212570.9940.0440.1490.925100
2.7-2.8411.50.12113070.9950.0370.1260.945100
2.84-3.0211.60.112870.9970.0310.1040.99100
3.02-3.2511.50.08212860.9980.0250.0861.11100
3.25-3.5811.50.06712900.9980.020.071.166100
3.58-4.0911.40.0512880.9990.0150.0521.206100
4.09-5.1611.40.04413050.9990.0140.0471.259100
5.16-5010.80.04813480.9990.0150.0511.70699.7

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
DMphasing
MLPHAREphasing
REFMAC5.8.0107refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / FOM work R set: 0.977 / SU B: 4.577 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 1266 4.9 %RANDOM
Rwork0.1356 ---
obs0.1371 24340 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.65 Å2 / Biso mean: 32.68 Å2 / Biso min: 14.84 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 27 276 2196
Biso mean--28.31 43.94 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191973
X-RAY DIFFRACTIONr_bond_other_d0.0020.021867
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9782683
X-RAY DIFFRACTIONr_angle_other_deg0.98734274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67922.97684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36715294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5221517
X-RAY DIFFRACTIONr_chiral_restr0.1060.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
X-RAY DIFFRACTIONr_mcbond_it1.1061.669999
X-RAY DIFFRACTIONr_mcbond_other1.0951.667998
X-RAY DIFFRACTIONr_mcangle_it1.7672.491247
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 97 -
Rwork0.216 1794 -
all-1891 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7882-0.42592.12271.6041-0.1692.72460.0393-0.04460.21470.12210.011-0.2317-0.21210.1953-0.05020.0781-0.05140.03410.0642-0.00090.142763.67371.86731.223
214.07981.6266-7.007612.1664-8.976729.61950.37080.21080.6895-0.30770.41450.4603-0.7795-0.2298-0.78520.1731-0.03580.02190.09980.14270.240955.4686.73219.266
32.2749-0.01360.36281.85980.07791.8491-0.07830.06750.5837-0.01260.041-0.2517-0.32840.22150.03720.1253-0.08640.01040.07630.02480.257864.31483.23329.024
42.04990.0867-0.03632.6601-0.45961.1248-0.0101-0.08160.3840.0521-0.00160.0589-0.23370.03130.01180.0939-0.00790.02170.0361-0.00880.128549.8478.27933.368
59.7064-3.0214.38541.95642.173714.4785-0.4898-0.9908-0.04730.37990.48440.01480.58730.40740.00540.14770.12570.05660.47890.07760.112150.91757.36644.619
61.9339-0.5990.07010.81990.03820.4364-0.0334-0.2290.1020.16040.0374-0.1236-0.10690.0758-0.0040.081-0.0264-0.00080.0814-0.00210.082258.97163.89836.568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 34
2X-RAY DIFFRACTION2A35 - 40
3X-RAY DIFFRACTION3A41 - 103
4X-RAY DIFFRACTION4A104 - 144
5X-RAY DIFFRACTION5A145 - 159
6X-RAY DIFFRACTION6A160 - 248

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