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- PDB-2p8j: Crystal structure of S-adenosylmethionine-dependent methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 2p8j
TitleCrystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) from Clostridium acetobutylicum at 2.00 A resolution
ComponentsS-adenosylmethionine-dependent methyltransferase
KeywordsTRANSFERASE / NP_349143.1 / S-adenosylmethionine-dependent methyltransferase / Methyltransferase domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function
: / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / S-adenosylmethionine-dependent methyltransferase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) from Clostridium acetobutylicum at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 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 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY 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: S-adenosylmethionine-dependent methyltransferase
B: S-adenosylmethionine-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,22016
Polymers48,8192
Non-polymers1,40114
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-54 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.860, 83.860, 159.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSILEILE6AA2 - 53 - 6
21LYSLYSILEILE6BB2 - 53 - 6
32ARGARGGLUGLU4AA6 - 1507 - 151
42ARGARGGLUGLU4BB6 - 1507 - 151
53GLUGLUVALVAL6AA153 - 155154 - 156
63GLUGLUVALVAL6BB153 - 155154 - 156
74ILEILEARGARG4AA156 - 184157 - 185
84ILEILEARGARG4BB156 - 184157 - 185
95ASNASNILEILE6AA186 - 191187 - 192
105ASNASNILEILE6BB186 - 191187 - 192
116LYSLYSSERSER4AA192 - 204193 - 205
126LYSLYSSERSER4BB192 - 204193 - 205
137LYSLYSLEULEU6AA205 - 208206 - 209
147LYSLYSILEILE6BB205 - 207206 - 208
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein S-adenosylmethionine-dependent methyltransferase


Mass: 24409.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: DSM 792, JCM 1419, LMG 5710, VKM B-1787 / Gene: NP_349143.1, CA_C2531 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97G40

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: NANODROP, 0.2M (NH4)2SO4, 10.0% Glycerol, 20.0% PEG 300, 0.1M Phosphate Citrate pH 4.2, 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: 0.91162, 0.97908, 0.97879
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 18, 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
10.911621
20.979081
30.978791
ReflectionResolution: 2→29.975 Å / Num. obs: 44338 / % possible obs: 99.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.044 / Χ2: 0.968 / Net I/σ(I): 21.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2-2.054.90.3253.0931150.9499.6
2.05-2.114.90.25631181.06999.8
2.11-2.174.90.20731330.94799.8
2.17-2.244.90.16931291.08299.8
2.24-2.324.90.13631340.986100
2.32-2.4150.11931500.976100
2.41-2.5250.10131550.96100
2.52-2.6550.07831540.94100
2.65-2.8250.06431500.989100
2.82-3.0450.04931840.943100
3.04-3.344.90.0431870.957100
3.34-3.834.90.03532100.89999.9
3.83-4.824.90.02932330.95999.6
4.82-504.70.03232870.90996.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.634 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.123
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ELECTRON DENSITIES CORRESPONDING TO RESIDUES A1 AND A151 WERE NOT MODELED. 5. POLYETHYLENE GLYCOL, SULFATE AND GLYCEROL MOLECULES FROM THE CRYSTALLIZATION SOLUTIONS WERE MODELED INTO THE STRUCTURE. 6. RESIDUE LYS B6 IS A RAMACHANDRAN OUTLIER AND IS IN A REGION OF DISORDERED ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2229 5 %RANDOM
Rwork0.165 ---
all0.167 ---
obs0.167 44263 99.53 %-
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: 43.522 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å20 Å2
2---0.17 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 88 318 3693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223493
X-RAY DIFFRACTIONr_bond_other_d0.0010.023209
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9964678
X-RAY DIFFRACTIONr_angle_other_deg0.7837487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63224.724163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55215642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5931518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02698
X-RAY DIFFRACTIONr_nbd_refined0.1880.2653
X-RAY DIFFRACTIONr_nbd_other0.1830.23169
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21662
X-RAY DIFFRACTIONr_nbtor_other0.0840.22043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.224
X-RAY DIFFRACTIONr_mcbond_it1.88132168
X-RAY DIFFRACTIONr_mcbond_other0.5883860
X-RAY DIFFRACTIONr_mcangle_it2.67753344
X-RAY DIFFRACTIONr_scbond_it4.76181532
X-RAY DIFFRACTIONr_scangle_it6.477111324
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2829MEDIUM POSITIONAL0.290.5
200LOOSE POSITIONAL1.285
2829MEDIUM THERMAL0.882
200LOOSE THERMAL8.6410
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 158 -
Rwork0.21 3061 -
obs-3219 99.26 %
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)
11.8980.43080.00442.5061-0.56033.3285-0.04750.39940.1165-0.41540.03520.2054-0.23130.0740.0123-0.02590.0826-0.1052-0.1914-0.0044-0.22075.78561.0693.748
21.5666-0.9150.47224.1976-0.12560.6744-0.0429-0.0113-0.03120.09290.0514-0.18710.03880.0794-0.0086-0.18680.1018-0.0108-0.2909-0.0045-0.269813.96653.22629.066
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 2013 - 202
22BB1 - 2012 - 202

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