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- PDB-3ggd: Crystal structure of SAM-dependent methyltransferase (YP_325210.1... -

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Basic information

Entry
Database: PDB / ID: 3ggd
TitleCrystal structure of SAM-dependent methyltransferase (YP_325210.1) from ANABAENA VARIABILIS ATCC 29413 at 2.11 A resolution
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / YP_325210.1 / SAM-dependent methyltransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


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
: / IMIDAZOLE / S-ADENOSYL-L-HOMOCYSTEINE / Unknown ligand / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.11 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SAM-dependent methyltransferase (YP_325210.1) from ANABAENA VARIABILIS ATCC 29413 at 2.11 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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 / _pdbx_entry_details.has_protein_modification

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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)29,25419
Polymers27,7631
Non-polymers1,49118
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.520, 112.520, 112.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsTHE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SAM-dependent methyltransferase


Mass: 27763.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Gene: Ava_4718, YP_325210.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M3X1

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Non-polymers , 8 types, 210 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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

CrystalDescription: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND .
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01M cobalt chloride, 1.8M ammonium sulfate, 0.1M MES pH 6.5, ADDITIVE: 0.001 M S-ADENOSYLMETHIONINE (SAM), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97967
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
ReflectionResolution: 2.11→30.083 Å / Num. obs: 42096 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 17.9 % / Biso Wilson estimate: 40.16 Å2 / Rmerge(I) obs: 0.221 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.11-2.191.532644988394199.6
2.19-2.271.152.7548737150199.4
2.27-2.380.913.5648618442199.7
2.38-2.50.674.9589897574199.8
2.5-2.660.816.3720148105199.8
2.66-2.860.658.4755147751199.8
2.86-3.150.5312.2879687989199.6
3.15-3.60.3217.8889707903199.9
3.6-4.530.1524.2908667956199.8
4.53-30.0830.0927.8936598021199.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.11→30.083 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.175 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.S-ADENOSYLMETHIONINE WAS ADDED DURING CRYSTALLIZATION. IN THIS STRUCTURE, ONLY S-ADENOSYL-L-HOMOCYSTEINE( SAH) IS MODELED IN THE CONSERVED BINDING SITE DUE TO A POSSIBLE ENZYMATICALLY RELATED DEGRADATION. AN UNKNOWN LIGAND (UNL) IS MODELED NEXT TO THE S-ADENOSYL-L- HOMOCYSTEINE IN THE SAME BINDING SITE. THE SHAPE OF THE LIGAND IS CREATINE LIKE. 5.A COBALT ION FROM THE CRYSTALLIZATION REAGENT IS MODELED IN THIS STRUCTURE. THE PRESENCE OF THE CO ATOM IS SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS AND GEOMETRY. ADDITIONAL ELECTRON DENSITY IS OBSERVED ADJACENT TO THE COBALT ION AND NEAR TO RESIDUES 203 AND 243. THIS DENSITY WAS LEFT UNMODELED. 6.AN IMIDAZOLE MOLECULE AND CHLORIDE ION FROM THE PROTEIN BUFFER, SULFATE IONS FROM THE CRYSTALLIZATION CONDITION AND ETHYLENE GLYCOL MOLECULES FROM THE CRYOPROTECTANT ARE ALSO MODELED IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 2128 5.1 %RANDOM
Rwork0.162 ---
obs0.163 42037 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 138.09 Å2 / Biso mean: 63.133 Å2 / Biso min: 40.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.95 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.11→30.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 98 192 2202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222116
X-RAY DIFFRACTIONr_bond_other_d0.0020.021424
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9992875
X-RAY DIFFRACTIONr_angle_other_deg0.94733471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2515258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85424.34892
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28715330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2861510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022342
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02428
X-RAY DIFFRACTIONr_nbd_refined0.2160.3425
X-RAY DIFFRACTIONr_nbd_other0.2040.31545
X-RAY DIFFRACTIONr_nbtor_refined0.1870.51001
X-RAY DIFFRACTIONr_nbtor_other0.0890.5969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5293
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0430.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.512
X-RAY DIFFRACTIONr_mcbond_it0.9231.51326
X-RAY DIFFRACTIONr_mcbond_other0.2171.5505
X-RAY DIFFRACTIONr_mcangle_it1.30222048
X-RAY DIFFRACTIONr_scbond_it2.3013937
X-RAY DIFFRACTIONr_scangle_it3.2044.5827
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 177 -
Rwork0.205 2863 -
all-3040 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: 12.5878 Å / Origin y: 41.096 Å / Origin z: 7.2816 Å
111213212223313233
T-0.171 Å20.0016 Å2-0.0059 Å2--0.1496 Å20.0114 Å2---0.176 Å2
L1.7105 °2-0.0314 °2-0.3779 °2-1.9002 °20.8043 °2--1.424 °2
S-0.0058 Å °-0.0891 Å °-0.2023 Å °0.0267 Å °-0.0809 Å °-0.0527 Å °0.087 Å °-0.0175 Å °0.0867 Å °

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