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- PDB-3dlc: Crystal structure of a putative s-adenosyl-l-methionine-dependent... -

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Basic information

Entry
Database: PDB / ID: 3dlc
TitleCrystal structure of a putative s-adenosyl-l-methionine-dependent methyltransferase (mmp1179) from methanococcus maripaludis at 1.15 A resolution
ComponentsPutative S-adenosyl-L-methionine-dependent Methyltransferase
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Arsenite methyltransferase-like / Methyltransferase type 11 / 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
ACETATE ION / S-ADENOSYLMETHIONINE / SAM (And some other nucleotide) binding motif:Generic methyltransferase
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative S-adenosyl-L-methionine-dependent Methyltransferase (NP_988299.1) from Methanococcus maripaludis JJ (DSM 2067) at 1.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative S-adenosyl-L-methionine-dependent Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3995
Polymers24,7571
Non-polymers6424
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.610, 63.500, 75.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative S-adenosyl-L-methionine-dependent Methyltransferase


Mass: 24757.426 Da / Num. of mol.: 1 / Mutation: N45T, D89N, T127A, V194I, E202G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: JJ [DSM 2067] / Gene: NP_988299.1, MMP1179 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6LY14
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
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. THE STRAIN CLONED, METHANOCOCCUS MARIPALUDIS JJ, DIFFERS FROM THE DATABASE SEQUENCE STRAIN, METHANOCOCCUS MARIPALUDIS S2. DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS THE CONSTRUCT HAS THE FOLLOWING SEQUENCE DIFFERENCES WHEN COMPARED TO THE DATABASE SEQUENCE: N45T, D89N, T127A, V194I AND E202G. THESE SEQUENCE DIFFERENCES ARE SUPPORTED BY THE ELECTRON DENSITY.

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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: 1.92 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.17M ammonium acetate, 15.0% Glycerol, 25.5% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, Additive - 1mM S-adenosylmethionine, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97947
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979471
ReflectionResolution: 1.15→29.26 Å / Num. obs: 68022 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 7.892 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.15-1.190.3782.3212331198894.2
1.19-1.240.3232.7240471335597.2
1.24-1.30.2753.2245461344797.8
1.3-1.360.2174209331131498.5
1.36-1.450.1675.1253551360698.8
1.45-1.560.117.4238641274398.8
1.56-1.720.07410.3248871314399
1.72-1.970.04615244341290398.7
1.97-2.480.03824.2354061288499.3
2.480.02539.8494181276397.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.15→29.26 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.958 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.031
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. S-ADENOSYLMETHIONINE (SAM), ACETATE (ACT) AND GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.138 3439 5.1 %RANDOM
Rwork0.12 ---
obs0.121 67971 99.46 %-
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 mean: 9.085 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.15→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 43 328 2093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222033
X-RAY DIFFRACTIONr_bond_other_d0.0030.021435
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9782786
X-RAY DIFFRACTIONr_angle_other_deg1.34233547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9885285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03824.95101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66515394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.481514
X-RAY DIFFRACTIONr_chiral_restr0.1140.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022326
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02412
X-RAY DIFFRACTIONr_mcbond_it1.77621208
X-RAY DIFFRACTIONr_mcbond_other0.8562492
X-RAY DIFFRACTIONr_mcangle_it2.57541985
X-RAY DIFFRACTIONr_scbond_it3.9196825
X-RAY DIFFRACTIONr_scangle_it5.128769
X-RAY DIFFRACTIONr_rigid_bond_restr2.21733468
X-RAY DIFFRACTIONr_sphericity_free7.5593338
X-RAY DIFFRACTIONr_sphericity_bonded3.36933404
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 245 -
Rwork0.178 4598 -
all-4843 -
obs--97.25 %

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