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- PDB-5lhm: Crystal Structure of SafC from Myxococcus xanthus apo-Form -

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Basic information

Entry
Database: PDB / ID: 5lhm
TitleCrystal Structure of SafC from Myxococcus xanthus apo-Form
ComponentsPutative O-methyltransferase
KeywordsTRANSFERASE / O-METHYL TRANSFERASE / SAM
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / Putative O-methyltransferase
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.31 Å
AuthorsGerhardt, S. / Netzer, J. / Einsle, O.
CitationJournal: FEBS Lett. / Year: 2017
Title: Functional and structural characterisation of a bacterial O-methyltransferase and factors determining regioselectivity.
Authors: Siegrist, J. / Netzer, J. / Mordhorst, S. / Karst, L. / Gerhardt, S. / Einsle, O. / Richter, M. / Andexer, J.N.
History
DepositionJul 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Source and taxonomy
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7989
Polymers26,2631
Non-polymers5358
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-8 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.558, 64.558, 118.163
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative O-methyltransferase


Mass: 26262.963 Da / Num. of mol.: 1 / Mutation: A77T
Source method: isolated from a genetically manipulated source
Details: Mutation A77T / Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: safC / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q50859
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.71 Å3/Da / Density % sol: 54.61 % / Mosaicity: 0.14 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG MME 5000, Sodium Acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 31, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.31→118.16 Å / Num. obs: 69174 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 13.71 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.144 / Rsym value: 0.152 / Net I/σ(I): 12.6
Reflection shellResolution: 1.311→1.38 Å / Redundancy: 20.3 % / Rmerge(I) obs: 1.274 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.405 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
autoPROCdata collection
BUSTER-TNT2.10.3refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HNK

2hnk


Resolution: 1.31→19.18 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.044 / SU Rfree Blow DPI: 0.045 / SU Rfree Cruickshank DPI: 0.044
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3376 4.9 %RANDOM
Rwork0.177 ---
obs0.178 68892 99.5 %-
Displacement parametersBiso max: 97.39 Å2 / Biso mean: 20.01 Å2 / Biso min: 7.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.0702 Å20 Å20 Å2
2--0.0702 Å20 Å2
3----0.1404 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.31→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 33 205 1915
Biso mean--35.06 35.18 -
Num. residues----213
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d671SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes274HARMONIC5
X-RAY DIFFRACTIONt_it1806HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion246SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2327SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1806HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2461HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion16.15
LS refinement shellResolution: 1.31→1.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 268 5.39 %
Rwork0.256 4706 -
all-4974 -
obs--97.74 %
Refinement TLS params.Method: refined / Origin x: -24.1514 Å / Origin y: 11.6635 Å / Origin z: -12.7711 Å
111213212223313233
T0.0021 Å2-0.009 Å2-0.001 Å2--0.0131 Å2-0.0065 Å2---0.0273 Å2
L0.0774 °20.0515 °2-0.0878 °2-0.3769 °20.0092 °2--0.7454 °2
S0.0107 Å °-0.0039 Å °0.0059 Å °0.0212 Å °-0.0256 Å °0.0022 Å °-0.0582 Å °0.0265 Å °0.0148 Å °
Refinement TLS groupSelection details: { A|* }

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