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- PDB-2i6g: Crystal structure of a putative methyltransferase (tehb, stm1608)... -

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Basic information

Entry
Database: PDB / ID: 2i6g
TitleCrystal structure of a putative methyltransferase (tehb, stm1608) from salmonella typhimurium lt2 at 1.90 A resolution
ComponentsPutative methyltransferase
KeywordsTRANSFERASE / S-adenosyl-l-methionine-dependent methyltransferase fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


response to tellurium ion / S-adenosylmethionine-dependent methyltransferase activity / methyltransferase activity / methylation / cytoplasm
Similarity search - Function
Tellurite resistance methyltransferase, TehB / Tellurite resistance methyltransferase TehB-like domain / Tellurite resistance protein TehB / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Putative methyltransferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of putative METHYLTRANSFERASE (16420133) from SALMONELLA TYPHIMURIUM LT2 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 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
Remark 999SEQUENCE THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION. THE CONSTRUCT WAS ...SEQUENCE THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION. 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: Putative methyltransferase
B: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,49316
Polymers45,6852
Non-polymers80814
Water6,990388
1
A: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3119
Polymers22,8431
Non-polymers4688
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1827
Polymers22,8431
Non-polymers3406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.889, 60.155, 72.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-400-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYASPAA0 - 1371 - 138
21GLYASPBB0 - 1371 - 138
32PHEGLYAA147 - 173148 - 174
42PHEGLYBB147 - 173148 - 174
53MLYALAAA186 - 198187 - 199
63MLYALABB186 - 198187 - 199

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Components

#1: Protein Putative methyltransferase


Mass: 22842.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: 16420133 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZPC3
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.29 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5
Details: 0.2M NaOAc, 30.0% PEG-4000, 0.1M TRIS pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97927,0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 2, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979271
30.979131
ReflectionResolution: 1.8→29.604 Å / Num. obs: 35397 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.953.70.6241.2948625840.624100
1.95-23.70.481.6928625250.48100
2-2.063.70.4091.8904324560.409100
2.06-2.123.70.3692863523540.369100
2.12-2.193.70.2972.5848723130.297100
2.19-2.273.70.272.7818422250.27100
2.27-2.363.70.2153.4790221530.215100
2.36-2.453.70.23.7763520710.2100
2.45-2.563.70.1854737420050.185100
2.56-2.693.70.1564.6707119340.156100
2.69-2.833.70.1315.4661718120.131100
2.83-33.60.115.9640817570.11100
3-3.213.60.0986.2585416110.098100
3.21-3.473.60.0798557415380.079100
3.47-3.83.60.06110.5506914140.061100
3.8-4.253.60.0579.2457912880.057100
4.25-4.913.50.05610.3404211460.056100
4.91-6.013.50.078.134229880.07100
6.01-8.53.40.0746.926437800.074100
8.5-29.613.10.0577.813764430.05796.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.604 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.19 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1).HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2).THIS PROTEIN IS REDUCTIVELY METHYLATED. HOWEVER, DENSITY FOR MOST SOME OF THE METHYL GROUPS ARE NOT OBSERVED, MAYBE DUE TO FLEXIBILITY ...Details: 1).HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2).THIS PROTEIN IS REDUCTIVELY METHYLATED. HOWEVER, DENSITY FOR MOST SOME OF THE METHYL GROUPS ARE NOT OBSERVED, MAYBE DUE TO FLEXIBILITY OR LIMITED RESOLUTION. 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).ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 5).ELECTRON DENSITIES FOR RESIDUES A138-A146 AND A174-A185 WERE DISORDERED AND THESE REGIONS WERE NOT MODELED. 6). ACETATE AND CHLORIDE ANIONS FROM THE CRYSTALLIZATION BUFFER AND ETHYLENE GLYCOL CRYOPROTECTANT MOLECULES WERE MODELED INTO THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1770 5 %RANDOM
Rwork0.19 ---
obs0.192 35356 99.92 %-
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: 29.425 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2---0.62 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 50 388 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223090
X-RAY DIFFRACTIONr_bond_other_d0.0020.022886
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9994182
X-RAY DIFFRACTIONr_angle_other_deg0.82536638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8525392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23523.688141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90415442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4961524
X-RAY DIFFRACTIONr_chiral_restr0.1640.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02648
X-RAY DIFFRACTIONr_nbd_refined0.2070.3616
X-RAY DIFFRACTIONr_nbd_other0.1870.32990
X-RAY DIFFRACTIONr_nbtor_refined0.1830.51482
X-RAY DIFFRACTIONr_nbtor_other0.0870.51837
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5500
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0660.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.377
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.537
X-RAY DIFFRACTIONr_mcbond_it0.94321968
X-RAY DIFFRACTIONr_mcbond_other0.2422789
X-RAY DIFFRACTIONr_mcangle_it1.40733045
X-RAY DIFFRACTIONr_scbond_it1.24531282
X-RAY DIFFRACTIONr_scangle_it1.67931128
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2542 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.470.5
MEDIUM THERMAL0.582
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 134 -
Rwork0.257 2446 -
obs-2580 99.96 %
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)
11.2664-0.6250.48562.1936-0.20861.73490.022-0.04760.1316-0.0933-0.0645-0.3283-0.02130.11350.0425-0.2753-0.01160.0129-0.20250.0186-0.107633.7234.62229.337
21.33880.3831-0.40920.4598-0.5431.2078-0.18510.0256-0.1439-0.24450.0967-0.1029-0.00880.10760.08840.0242-0.06510.0036-0.2064-0.0021-0.12934.20527.1716.177
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 1371 - 138
21AA147 - 173148 - 174
31AA186 - 198187 - 199
42BB0 - 1981 - 199

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