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- PDB-3lcc: Structure of a SAM-dependent halide methyltransferase from Arabid... -

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Basic information

Entry
Database: PDB / ID: 3lcc
TitleStructure of a SAM-dependent halide methyltransferase from Arabidopsis thaliana
ComponentsPutative methyl chloride transferase
KeywordsTRANSFERASE / Halide Methyltransferase
Function / homology
Function and homology information


: / thiol S-methyltransferase activity / glucosinolate catabolic process / defense response / methylation / plasma membrane / cytosol
Similarity search - Function
Thiopurine S-methyltransferase (TPMT) / TPMT family / Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Thiocyanate methyltransferase 1 / Thiocyanate methyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSchmidberger, J.W. / O'Hagan, D. / Naismith, J.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Halomethane Biosynthesis: Structure of a SAM-Dependent Halide Methyltransferase from Arabidopsis thaliana
Authors: Schmidberger, J.W. / James, A.B. / Edwards, R. / Naismith, J.H. / O'Hagan, D.
History
DepositionJan 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 methyl chloride transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8063
Polymers26,3861
Non-polymers4202
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.430, 54.430, 263.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Putative methyl chloride transferase / Halide/Thiol Methyltransferase 1 / AtHTMT1


Mass: 26385.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AtHOL1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II (DE3)
References: UniProt: O80561, UniProt: Q0WP12*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.14 Å3/Da / Density % sol: 42.39 % / Mosaicity: 0.6 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.0M (NH4)2SO4, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.8→47.137 Å / Num. all: 22767 / Num. obs: 22767 / % possible obs: 100 % / Redundancy: 7.6 % / Rsym value: 0.108
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 7.9 / Num. unique all: 3197 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.52 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.13 Å
Translation2.5 Å47.13 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 22653
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.9-100510.358505
5.38-6.951.40.71511
4.65-5.3849.10.798508
4.19-4.6543.40.79506
3.85-4.1949.70.804545
3.58-3.8547.60.793588
3.36-3.5854.40.779614
3.18-3.36580.797654
3.02-3.1865.90.755667
2.89-3.0288.30.735728
2.77-2.8989.20.665724
2.66-2.7789.30.751793
2.57-2.66920.7783
2.49-2.5793.30.502798
2.41-2.4991.40.697876
2.34-2.4190.80.711865
2.27-2.3488.60.36870
2.21-2.2789.20.729934
2.16-2.2189.70.714923
2.11-2.1691.50.65944
2.06-2.1186.60.625987
2.02-2.0688.80.554986
1.97-2.0288.20.5651026
1.94-1.9791.50.6791038
1.9-1.9486.80.5661053
1.86-1.989.10.5211075
1.83-1.8689.90.5571077
1.8-1.8388.60.6261075

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GB4

2gb4


Resolution: 1.8→19.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.145 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.924 / SU B: 4.209 / SU ML: 0.06 / SU R Cruickshank DPI: 0.104 / SU Rfree: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.177 1159 5.1 %RANDOM
Rwork0.149 ---
obs0.151 22625 99.99 %-
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 max: 40.49 Å2 / Biso mean: 8.351 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 27 198 1922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221814
X-RAY DIFFRACTIONr_bond_other_d0.0010.021232
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9832479
X-RAY DIFFRACTIONr_angle_other_deg0.83633021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22624.47476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04715290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.867157
X-RAY DIFFRACTIONr_chiral_restr0.0730.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02355
X-RAY DIFFRACTIONr_mcbond_it0.5581.51108
X-RAY DIFFRACTIONr_mcbond_other0.1291.5440
X-RAY DIFFRACTIONr_mcangle_it1.05821806
X-RAY DIFFRACTIONr_scbond_it1.753706
X-RAY DIFFRACTIONr_scangle_it2.9514.5673
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 77 -
Rwork0.17 1530 -
all-1607 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -5.3699 Å / Origin y: 20.8207 Å / Origin z: 12.5389 Å
111213212223313233
T0.0135 Å2-0.0076 Å2-0.0081 Å2-0.0054 Å20.0068 Å2--0.0177 Å2
L0.774 °20.1099 °2-0.1554 °2-0.6314 °2-0.1408 °2--0.8157 °2
S-0.0023 Å °-0.0048 Å °-0.0007 Å °0.0036 Å °-0.0159 Å °0.0029 Å °-0.0334 Å °0.008 Å °0.0181 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 228
2X-RAY DIFFRACTION1A300 - 301
3X-RAY DIFFRACTION1A236 - 435

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