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- PDB-6tgf: Pantoea stewartii WceF is a glycan biofilm modifying enzyme with ... -

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Basic information

Entry
Database: PDB / ID: 6tgf
TitlePantoea stewartii WceF is a glycan biofilm modifying enzyme with a bacteriophage tailspike-like parallel beta-helix fold
ComponentsExopolysaccharide biosynthesis protein
KeywordsHYDROLASE / WceF / beta-helix / tailspike-like
Function / homologyBacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Pectin lyase fold / Pectin lyase fold/virulence factor / Exopolysaccharide biosynthesis protein
Function and homology information
Biological speciesPantoea stewartii subsp. stewartii DC283 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsIrmscher, T. / Roske, Y. / Gayk, I. / Heinemann, U. / Barbirz, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)BA 4046/1-2 Germany
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Pantoea stewartii WceF is a glycan biofilm-modifying enzyme with a bacteriophage tailspike-like fold.
Authors: Irmscher, T. / Roske, Y. / Gayk, I. / Dunsing, V. / Chiantia, S. / Heinemann, U. / Barbirz, S.
History
DepositionNov 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3May 15, 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

Downloads & links

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Assembly

Deposited unit
F: Exopolysaccharide biosynthesis protein
D: Exopolysaccharide biosynthesis protein
E: Exopolysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,52847
Polymers241,5333
Non-polymers2,99544
Water11,133618
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.179, 97.196, 128.949
Angle α, β, γ (deg.)90.000, 106.400, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21F
31E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114D10 - 710
2114F10 - 710
3114E10 - 710

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.212676, -0.609493, -0.763732), (0.628417, -0.513208, 0.584559), (-0.748238, -0.604264, 0.273869)-18.772499, 34.292839, -17.66748
3given(0.214924, 0.635201, -0.741841), (-0.622207, -0.496424, -0.605327), (-0.752772, 0.591678, 0.288533)-30.510151, -4.51891, -29.20952

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Components

#1: Protein Exopolysaccharide biosynthesis protein


Mass: 80510.883 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pantoea stewartii subsp. stewartii DC283 (bacteria)
Gene: wceF, CKS_2251 / Plasmid: pET23a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H3REJ8
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG3350, 0.2M Di-NH4-hydrogen-citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.55→48.6 Å / Num. obs: 74949 / % possible obs: 96.4 % / Redundancy: 3.82 % / CC1/2: 0.985 / Rrim(I) all: 0.0231 / Net I/σ(I): 6.77
Reflection shellResolution: 2.55→2.7 Å / Mean I/σ(I) obs: 1.02 / Num. unique obs: 10202 / CC1/2: 0.36 / Rrim(I) all: 0.1281 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→48.6 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.89 / SU B: 31.724 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.966 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 2100 2.8 %RANDOM
Rwork0.227 ---
obs0.2283 72847 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 797.42 Å2 / Biso mean: 44.855 Å2 / Biso min: 16.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å21.24 Å2
2--0.05 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: final / Resolution: 2.55→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15820 0 194 618 16632
Biso mean--79.7 38.08 -
Num. residues----2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01316385
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714628
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.63922171
X-RAY DIFFRACTIONr_angle_other_deg1.0631.57533977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64352042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2322.899897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.907152538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.88715100
X-RAY DIFFRACTIONr_chiral_restr0.0330.22073
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0218669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023539
Refine LS restraints NCS

Ens-ID: 1 / Number: 9511 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1DMEDIUM POSITIONAL0.610.5
2FMEDIUM POSITIONAL0.820.5
3EMEDIUM POSITIONAL0.70.5
1DMEDIUM THERMAL10.452
2FMEDIUM THERMAL5.72
3EMEDIUM THERMAL15.452
LS refinement shellResolution: 2.55→2.615 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.365 121 -
Rwork0.355 4223 -
obs--76.25 %
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)
10.2428-0.0972-0.36460.05720.13320.5601-0.0141-0.00160.0145-0.00570.015-0.01070.0278-0.0074-0.0010.1213-0.019-0.00970.0117-0.00360.0854-14.775220.3444-14.2543
20.7401-0.0517-0.4760.03510.02690.3245-0.052-0.02990.0243-0.02720.0220.01140.04740.01020.030.0726-0.0124-0.01530.0129-0.01070.1351-23.90736.2609-22.5107
30.30380.1217-0.41980.1319-0.0920.65530.00150.00870.00060.0276-0.0025-0.02110.035-0.01510.0010.0716-0.0196-0.0110.01640.03770.1172-9.5643.3414-10.3845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F38 - 736
2X-RAY DIFFRACTION2D34 - 736
3X-RAY DIFFRACTION3E46 - 735

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