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- PDB-4e2l: Crystal Structure of the periplasmic domain of mutant FepE LPS O-... -

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Basic information

Entry
Database: PDB / ID: 4e2l
TitleCrystal Structure of the periplasmic domain of mutant FepE LPS O-antigen chain length regulator protein
ComponentsFerric enterobactin (Enterochelin) transport
KeywordsMEMBRANE PROTEIN / FepE polysaccharride co-polymerase / wzz / inner membrane / periplasmic space
Function / homology
Function and homology information


protein tyrosine kinase activity / identical protein binding / plasma membrane
Similarity search - Function
Bacterial polysaccharide co-polymerase-like / FepE-like / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / Helix Hairpins - #210 / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Regulator of length of O-antigen component of lipopolysaccharide chains
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKalynych, S. / Yao, D. / Magee, J.D. / Cygler, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Characterization of Closely Related O-antigen Lipopolysaccharide (LPS) Chain Length Regulators.
Authors: Kalynych, S. / Yao, D. / Magee, J. / Cygler, M.
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric enterobactin (Enterochelin) transport
B: Ferric enterobactin (Enterochelin) transport
C: Ferric enterobactin (Enterochelin) transport
D: Ferric enterobactin (Enterochelin) transport
E: Ferric enterobactin (Enterochelin) transport
F: Ferric enterobactin (Enterochelin) transport
G: Ferric enterobactin (Enterochelin) transport
H: Ferric enterobactin (Enterochelin) transport
I: Ferric enterobactin (Enterochelin) transport


Theoretical massNumber of molelcules
Total (without water)278,0009
Polymers278,0009
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31570 Å2
ΔGint-144 kcal/mol
Surface area101240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.307, 141.257, 136.888
Angle α, β, γ (deg.)90.000, 107.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ferric enterobactin (Enterochelin) transport


Mass: 30888.943 Da / Num. of mol.: 9 / Fragment: periplasmic domain / Mutation: delta(258-264)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs0626, fepE, Z0728 / Plasmid: pF04 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XBV8

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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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5M KCl, 0.05M MOPS, 12% (w/v) PEG4K, 20% w/v glycerol, pH 7.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97937 Å
DetectorDetector: CCD / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.8→49.716 Å / Num. obs: 93614 / Observed criterion σ(I): 11.3 / Rsym value: 11.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.716 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.4 / σ(F): 0 / Phase error: 33.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2891 4108 5 %
Rwork0.2417 --
obs0.244 82221 86.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.268 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.8872 Å2-0 Å2-33.4662 Å2
2---10.7812 Å2-0 Å2
3----7.106 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16883 0 0 0 16883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917149
X-RAY DIFFRACTIONf_angle_d1.21223296
X-RAY DIFFRACTIONf_dihedral_angle_d18.4936258
X-RAY DIFFRACTIONf_chiral_restr0.0812789
X-RAY DIFFRACTIONf_plane_restr0.0052967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.88490.38323050.35015790X-RAY DIFFRACTION65
2.8849-3.00040.39343240.33196630X-RAY DIFFRACTION73
3.0004-3.13690.35653810.30037035X-RAY DIFFRACTION79
3.1369-3.30230.34543880.27077502X-RAY DIFFRACTION84
3.3023-3.50910.31484300.2537843X-RAY DIFFRACTION87
3.5091-3.780.29164520.23158284X-RAY DIFFRACTION93
3.78-4.16020.25914240.2028466X-RAY DIFFRACTION94
4.1602-4.76180.23054490.18158730X-RAY DIFFRACTION97
4.7618-5.99770.27774800.24178849X-RAY DIFFRACTION98
5.9977-49.72340.26944750.24638984X-RAY DIFFRACTION98

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