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- PDB-2w8b: Crystal structure of processed TolB in complex with Pal -

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Basic information

Entry
Database: PDB / ID: 2w8b
TitleCrystal structure of processed TolB in complex with Pal
Components
  • (PROTEIN TOLB) x 2
  • PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
KeywordsPROTEIN TRANSPORT/MEMBRANE PROTEIN / PROTEIN TRANSPORT MEMBRANE PROTEIN COMPLEX / TOL / PAL / TOLB / MEMBRANE / PALMITATE / PERIPLASM / BACTERIOCIN TRANSPORT / TRANSPORT PROTEIN/LIPOPROTEIN / CELL OUTER MEMBRANE / TRANSPORT / LIPOPROTEIN / CELL MEMBRANE / OUTER MEMBRANE / PROTEIN TRANSPORT-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / protein import / cell division site / cell outer membrane / protein transport / outer membrane-bounded periplasmic space / periplasmic space / cell cycle ...cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / protein import / cell division site / cell outer membrane / protein transport / outer membrane-bounded periplasmic space / periplasmic space / cell cycle / cell division / protein domain specific binding / protein-containing complex binding / protein-containing complex / membrane
Similarity search - Function
Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / Outer membrane protein, OmpA-like, conserved site / WD40-like beta propeller / WD40-like Beta Propeller Repeat / OmpA-like domain. ...Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / Outer membrane protein, OmpA-like, conserved site / WD40-like beta propeller / WD40-like Beta Propeller Repeat / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / 60s Ribosomal Protein L30; Chain: A; / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Tol-Pal system protein TolB / Peptidoglycan-associated lipoprotein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSharma, A. / Bonsor, D.A. / Kleanthous, C.
CitationJournal: Embo J. / Year: 2009
Title: Allosteric Beta-Propeller Signalling in Tolb and its Manipulation by Translocating Colicins.
Authors: Bonsor, D.A. / Hecht, O. / Vankemmelbeke, M. / Sharma, A. / Krachler, A.M. / Housden, N.G. / Lilly, K.J. / James, R. / Moore, G.R. / Kleanthous, C.
History
DepositionJan 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN TOLB
B: PROTEIN TOLB
C: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
D: PROTEIN TOLB
E: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
F: PROTEIN TOLB
G: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
H: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,27127
Polymers228,6228
Non-polymers1,64919
Water27,3651519
1
A: PROTEIN TOLB
H: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6548
Polymers57,1552
Non-polymers4986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-11.5 kcal/mol
Surface area24860 Å2
MethodPQS
2
D: PROTEIN TOLB
E: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4956
Polymers57,1552
Non-polymers3394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-10.1 kcal/mol
Surface area25210 Å2
MethodPQS
3
F: PROTEIN TOLB
G: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4405
Polymers57,1552
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-11.4 kcal/mol
Surface area25430 Å2
MethodPQS
4
B: PROTEIN TOLB
C: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6838
Polymers57,1552
Non-polymers5276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11.1 kcal/mol
Surface area24780 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.740, 89.240, 90.900
Angle α, β, γ (deg.)86.81, 89.81, 68.62
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 8 molecules ABDFCEGH

#1: Protein PROTEIN TOLB / TOL B


Mass: 43637.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A855
#2: Protein PROTEIN TOLB / TOL B


Mass: 43637.379 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A855
#3: Protein
PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN


Mass: 13518.095 Da / Num. of mol.: 4 / Fragment: RESIDUES 65-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A912

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Non-polymers , 4 types, 1538 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1519 / 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: 2.35 Å3/Da / Density % sol: 47.69 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1M SODIUM ACETATE PH 4.6, 17% PEG4000, 0.2M AMMONIUM SULPHATE, 20MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.86→45.74 Å / Num. obs: 176410 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.2
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.2 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HQS

2hqs


Resolution: 1.86→45.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.693 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 8843 5 %RANDOM
Rwork0.191 ---
obs0.194 167524 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.79 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.86→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15701 0 98 1519 17318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02216328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.95122241
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71152121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70324.354751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.212152518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.53615104
X-RAY DIFFRACTIONr_chiral_restr0.140.22398
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1021.510357
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.838216636
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.95535971
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6624.55574
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 631 -
Rwork0.356 12119 -
obs--94.25 %

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