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- PDB-2py6: Crystal structure of Methyltransferase FkbM (YP_546752.1) from Me... -

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Basic information

Entry
Database: PDB / ID: 2py6
TitleCrystal structure of Methyltransferase FkbM (YP_546752.1) from Methylobacillus flagellatus KT at 2.20 A resolution
ComponentsMethyltransferase FkbM
KeywordsTRANSFERASE / YP_546752.1 / Methyltransferase FkbM / 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
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #160 / Methyltransferase FkbM / Methyltransferase FkbM domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Vaccinia Virus protein VP39 / NAD(P)-binding Rossmann-like Domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #160 / Methyltransferase FkbM / Methyltransferase FkbM domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Vaccinia Virus protein VP39 / NAD(P)-binding Rossmann-like Domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Unknown ligand / Methyltransferase FkbM
Similarity search - Component
Biological speciesMethylobacillus flagellatus KT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Methyltransferase FkbM (YP_546752.1) from Methylobacillus flagellatus KT at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 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 1.6Jan 25, 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase FkbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9028
Polymers46,5121
Non-polymers3907
Water6,828379
1
A: Methyltransferase FkbM
hetero molecules

A: Methyltransferase FkbM
hetero molecules

A: Methyltransferase FkbM
hetero molecules

A: Methyltransferase FkbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,60832
Polymers186,0494
Non-polymers1,55928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)73.660, 119.170, 122.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyltransferase FkbM


Mass: 46512.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus KT (bacteria)
Species: Methylobacillus flagellatus / Strain: KT, DSM 6875 / Gene: YP_546752.1, Mfla_2648 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q1GXX6, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 386 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 0.214M Ammonium nitrate, 14.0% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97926, 0.97891
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979261
30.978911
ReflectionResolution: 2.15→29.788 Å / Num. obs: 29426 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.24 % / Biso Wilson estimate: 24.43 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.15-2.230.4242.294385583194.6
2.23-2.320.3552.694505467196.3
2.32-2.420.305388395144196.3
2.42-2.550.2693.396935609196.6
2.55-2.710.2094.394905475196.5
2.71-2.920.1595.495645530197.1
2.92-3.210.1097.894505412196.6
3.21-3.670.06512.395665416196.2
3.67-4.610.04117.597675421195.9
4.61-29.790.03718.8100595449194.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.788 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.375 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.171
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. CHLORIDE ION, ETHYLENE GLYCOL, POLYETHYLENE GLYCOL-3350 (PEG) AND ONE UNKNOWN LIGAND (UNL) ARE MODELED IN THE STRUCTURE. THE UNKNOWN LIGAND IS CLOSE TO RESIDUES 259 AND 342. 5. RESIDUES 1-13 AND 300-319 ARE DISORDERED AND NOT MODELED IN THE STRUCTURE. 6. THERE IS A RAMACHANDRAN VIOLATION ON RESIUDE 112 WITH CLEAR DENSITY SUPPORT.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1494 5.1 %RANDOM
Rwork0.166 ---
all0.169 ---
obs0.169 29425 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.849 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 31 379 3366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223070
X-RAY DIFFRACTIONr_bond_other_d0.0020.022805
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9574165
X-RAY DIFFRACTIONr_angle_other_deg1.06536455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0655377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.3322.819149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00715479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5551528
X-RAY DIFFRACTIONr_chiral_restr0.1150.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
X-RAY DIFFRACTIONr_nbd_refined0.1940.3612
X-RAY DIFFRACTIONr_nbd_other0.1740.32966
X-RAY DIFFRACTIONr_nbtor_refined0.1790.51491
X-RAY DIFFRACTIONr_nbtor_other0.0850.51740
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.5422
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.3103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.529
X-RAY DIFFRACTIONr_mcbond_it2.1332061
X-RAY DIFFRACTIONr_mcbond_other0.5233763
X-RAY DIFFRACTIONr_mcangle_it2.94653032
X-RAY DIFFRACTIONr_scbond_it4.97181294
X-RAY DIFFRACTIONr_scangle_it6.114111133
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 104 -
Rwork0.199 2021 -
obs-2125 97.7 %
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)
10.8776-0.0910.51514.2059-0.82450.46540.00160.0686-0.0515-0.25140.0187-0.28260.10390.117-0.0203-0.037-0.03910.0435-0.09930.01-0.160423.63223.75447.166
20.4743-0.67930.43132.0981-0.49881.64370.06290.0278-0.0544-0.05750.007-0.0880.19620.0731-0.0699-0.1373-0.02310.0315-0.1424-0.0097-0.112421.60612.75651.308
30.57810.01650.08390.51540.10360.6191-0.01920.04080.014-0.1563-0.020.08-0.0209-0.02890.0392-0.10240.0164-0.021-0.15390.0117-0.1754-7.31729.11644.556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 7516 - 76
2X-RAY DIFFRACTION2AA76 - 16577 - 166
3X-RAY DIFFRACTION3AA166 - 408167 - 409

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