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- PDB-3b8m: Structure of FepE- Bacterial Polysaccharide Co-polymerase -

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Basic information

Entry
Database: PDB / ID: 3b8m
TitleStructure of FepE- Bacterial Polysaccharide Co-polymerase
ComponentsFerric enterobactin (Enterochelin) transport
KeywordsBIOSYNTHETIC PROTEIN / WZZ / FepE / Bacterial Polysaccharide Co-polymerase / METAL TRANSPORT
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 / molecular replacement / Resolution: 2.7 Å
AuthorsTocilj, A. / Matte, A. / Cygler, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Bacterial polysaccharide co-polymerases share a common framework for control of polymer length
Authors: Tocilj, A. / Munger, C. / Proteau, A. / Morona, R. / Purins, L. / Ajamian, E. / Wagner, J. / Papadopoulos, M. / Van Den Bosch, L. / Rubinstein, J.L. / Fethiere, J. / Matte, A. / Cygler, M.
History
DepositionNov 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferric enterobactin (Enterochelin) transport
B: Ferric enterobactin (Enterochelin) transport
C: Ferric enterobactin (Enterochelin) transport


Theoretical massNumber of molelcules
Total (without water)95,5953
Polymers95,5953
Non-polymers00
Water50428
1
A: Ferric enterobactin (Enterochelin) transport
B: Ferric enterobactin (Enterochelin) transport
C: Ferric enterobactin (Enterochelin) transport

A: Ferric enterobactin (Enterochelin) transport
B: Ferric enterobactin (Enterochelin) transport
C: Ferric enterobactin (Enterochelin) transport

A: Ferric enterobactin (Enterochelin) transport
B: Ferric enterobactin (Enterochelin) transport
C: Ferric enterobactin (Enterochelin) transport


Theoretical massNumber of molelcules
Total (without water)286,7869
Polymers286,7869
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area33060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.726, 139.726, 276.654
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 64 - 330 / Label seq-ID: 13 - 279

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12CC
22AA

NCS ensembles :
ID
1
2

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Components

#1: Protein Ferric enterobactin (Enterochelin) transport


Mass: 31865.092 Da / Num. of mol.: 3 / Fragment: residues 65-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157 / Gene: fepE / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8XBV8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 4.09 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 298 K / pH: 7.5
Details: Sodium Citrate Na3C6H5O7, pH 7.5, vapor diffusion, temperature 298K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 44193 / % possible obs: 99.1 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.448 / % possible all: 92.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.29 Å49.15 Å
Translation3.29 Å49.15 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.13 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.213 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26947 2072 5 %RANDOM
Rwork0.22577 ---
obs0.22803 39284 92.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.932 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6133 0 0 28 6161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226250
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9818459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26825.655290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.034151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6941530
X-RAY DIFFRACTIONr_chiral_restr0.0890.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024619
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.32683
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.54360
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.5317
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.361
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.16733914
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.73666251
X-RAY DIFFRACTIONr_scbond_it3.35142577
X-RAY DIFFRACTIONr_scangle_it5.55682208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1020medium positional0.240.5
2C1020medium positional0.270.5
1B1021loose positional0.515
2C1020loose positional0.485
1B1020medium thermal0.712
2C1020medium thermal0.852
1B1021loose thermal2.3810
2C1020loose thermal2.1610
LS refinement shellResolution: 2.7→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 115 -
Rwork0.314 2245 -
obs--73.59 %

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