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- PDB-5mu5: Structure of MAf glycosyltransferase from Magnetospirillum magnet... -

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Basic information

Entry
Database: PDB / ID: 5mu5
TitleStructure of MAf glycosyltransferase from Magnetospirillum magneticum AMB-1
ComponentsUncharacterized protein
KeywordsTRANSFERASE / glycosyltransferase
Function / homologyGlycosyltransferase Maf, N-terminal / Flagellin glycosyltransferase Maf, helical bundle domain / Flagellin glycosyltransferase Maf helical bundle domain / Glycosyltransferase Maf N-terminal domain / 6-hydroxymethylpterin diphosphokinase MptE-like / 6-hydroxymethylpterin diphosphokinase MptE-like / TRIETHYLENE GLYCOL / DUF115 domain-containing protein
Function and homology information
Biological speciesMagnetospirillum magneticum AMB-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSulzenbacher, G. / Roig-Zamboni, V. / Murat, D. / Vincentelli, R. / Wu, L.F. / Guerardel, Y. / Alberto, F.
CitationJournal: Environ. Microbiol. / Year: 2018
Title: Glycosylate and move! The glycosyltransferase Maf is involved in bacterial flagella formation.
Authors: Sulzenbacher, G. / Roig-Zamboni, V. / Lebrun, R. / Guerardel, Y. / Murat, D. / Mansuelle, P. / Yamakawa, N. / Qian, X.X. / Vincentelli, R. / Bourne, Y. / Wu, L.F. / Alberto, F.
History
DepositionJan 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,92810
Polymers75,1681
Non-polymers7609
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-11 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.447, 126.852, 64.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 75168.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magneticum AMB-1 (bacteria)
Gene: amb0685 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): Rosetta pLys / References: UniProt: Q2W9I6

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Non-polymers , 6 types, 107 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.21 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.5-1.7 M (NH4)2SO4, 5% (v/v) polyethylene glycol 400 and 0.1 M MES buffer, pH 6.5-7.0
PH range: 6.5 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.3→45.3 Å / Num. obs: 43504 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.04 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6235 / Num. unique obs: 6235 / Rpim(I) all: 0.369 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
CRANKphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→45.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.053 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 2224 5.1 %RANDOM
Rwork0.18671 ---
obs0.18841 41238 99.46 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 50.766 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å2-0 Å2-0 Å2
2---2.28 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.3→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 46 98 5158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195162
X-RAY DIFFRACTIONr_bond_other_d0.0010.024883
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9686980
X-RAY DIFFRACTIONr_angle_other_deg0.759311199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5835629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1823.228254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46915852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8861549
X-RAY DIFFRACTIONr_chiral_restr0.0790.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 173 -
Rwork0.28 2961 -
obs--99.08 %
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)
11.1108-0.0852-0.18921.4310.02631.58610.0044-0.0119-0.0717-0.0139-0.00750.26830.089-0.13720.00310.01640.0073-0.00720.03730.01040.1241-29.83938.064642.1363
20.48550.1412-0.16240.9118-0.03120.67040.0064-0.0130.0683-0.04820.0334-0.0811-0.05530.1408-0.03980.0139-0.02160.00380.0412-0.00450.066114.073516.640330.2876
31.0760.6349-0.42820.7747-0.23780.98150.0926-0.22860.06980.1704-0.04860.0041-0.06630.1123-0.0440.1033-0.00680.0090.0706-0.01910.0494-3.05118.549361.1161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 85
2X-RAY DIFFRACTION1A118 - 238
3X-RAY DIFFRACTION2A261 - 531
4X-RAY DIFFRACTION3A90 - 117
5X-RAY DIFFRACTION3A239 - 260
6X-RAY DIFFRACTION3A532 - 664

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