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- PDB-1o54: Crystal structure of SAM-dependent O-methyltransferase (TM0748) f... -

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Basic information

Entry
Database: PDB / ID: 1o54
TitleCrystal structure of SAM-dependent O-methyltransferase (TM0748) from Thermotoga maritima at 1.65 A resolution
ComponentsSAM-dependent O-methyltransferase
KeywordsTRANSFERASE / TM0748 / SAM-DEPENDENT O-METHYLTRANSFERASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


tRNA (adenine58-N1)-methyltransferase / : / tRNA (m1A) methyltransferase complex / tRNA methylation
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA (adenine(58)-N(1))-methyltransferase TrmI
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SAM-dependent O-methyltransferase (TM0748) from Thermotoga maritima at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM-dependent O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6152
Polymers31,5791
Non-polymers351
Water5,314295
1
A: SAM-dependent O-methyltransferase
hetero molecules

A: SAM-dependent O-methyltransferase
hetero molecules

A: SAM-dependent O-methyltransferase
hetero molecules

A: SAM-dependent O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4608
Polymers126,3184
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)64.253, 74.992, 143.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-267-

HOH

21A-276-

HOH

31A-280-

HOH

41A-316-

HOH

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Components

#1: Protein SAM-dependent O-methyltransferase


Mass: 31579.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0748 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZK7, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.57 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 40% MPD, 0.1M sodium acetate trihydrate, pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.976224
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2003 / Details: flat mirror
RadiationMonochromator: single crystal Si(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976224 Å / Relative weight: 1
ReflectionResolution: 1.65→35.93 Å / Num. all: 40334 / Num. obs: 40334 / % possible obs: 95.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 31.78 Å2 / Rsym value: 0.055 / Net I/σ(I): 17.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 4754 / Rsym value: 0.433 / % possible all: 78.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I9G

1i9g


Resolution: 1.65→35.93 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.17 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1, RESIDUES A77-79 HAVE AMBIGUOUS DIFFERENCE DENSITY AROUND THEM AND MAY BE MISTRACED; RESIDUE A78 WAS OMITTED. RESIDUE A163 HAS AMBIGUOUS SIDECHAIN DENSITY. RESIDUES A147-148 MAY HAVE AN ...Details: 1, RESIDUES A77-79 HAVE AMBIGUOUS DIFFERENCE DENSITY AROUND THEM AND MAY BE MISTRACED; RESIDUE A78 WAS OMITTED. RESIDUE A163 HAS AMBIGUOUS SIDECHAIN DENSITY. RESIDUES A147-148 MAY HAVE AN ALTERNATIVE BACKBONE CONFORMATION, THAT WAS TOO AMBIGUOUS TO TRACE. THE ATOM 1 WAS BUILT AS CHLORINE BECAUSE IT PROVIDES THE BEST ELECTRONIC FIT FOR THE DIFFERENCE DENSITY, WHILE DISTANCES TO NEIGHBOURING WATERS ARE TOO LARGE FOR ISOELECTRONIC CATIONS. A POSSIBLE EXPLANATION FOR ITS PRESENCE IN THE UNCHARGED SITE IS THE LIKELY DIPOLE OF THE ADJACENT HELIX. 2, HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18762 2036 5 %RANDOM
Rwork0.15768 ---
obs0.15918 38297 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--1.31 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 1.65→35.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 1 295 2386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222155
X-RAY DIFFRACTIONr_bond_other_d0.0010.022004
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9552912
X-RAY DIFFRACTIONr_angle_other_deg0.75534657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.18623.93999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12715392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.531516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined0.210.2393
X-RAY DIFFRACTIONr_nbd_other0.1810.22008
X-RAY DIFFRACTIONr_nbtor_other0.0820.21268
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.2238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.240
X-RAY DIFFRACTIONr_mcbond_it0.9591.51321
X-RAY DIFFRACTIONr_mcangle_it1.75922142
X-RAY DIFFRACTIONr_scbond_it2.5223834
X-RAY DIFFRACTIONr_scangle_it4.324.5770
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 121 5.38 %
Rwork0.277 2128 -
Refinement TLS params.Method: refined / Origin x: 8.823 Å / Origin y: 32.636 Å / Origin z: 20.851 Å
111213212223313233
T-0.1419 Å20.0143 Å2-0.0017 Å2--0.0695 Å2-0.0001 Å2---0.0558 Å2
L0.1862 °20.2131 °2-0.0032 °2-0.834 °2-0.0158 °2--0.6055 °2
S-0.0096 Å °-0.0225 Å °-0.0518 Å °0.0403 Å °0.027 Å °-0.1607 Å °0.065 Å °0.0973 Å °-0.0173 Å °
Refinement TLS groupSelection: ALL

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