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- PDB-7zc8: Crystal structure of the C-terminal domain of FusB, a TonB homologue -

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Basic information

Entry
Database: PDB / ID: 7zc8
TitleCrystal structure of the C-terminal domain of FusB, a TonB homologue
ComponentsProtein TonB
KeywordsPROTEIN TRANSPORT / TonB / periplasm / bacterial iron uptake / ferredoxin uptake
Function / homology
Function and homology information


siderophore-iron transmembrane transporter activity / energy transducer activity / membrane => GO:0016020 / protein transport / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
Gram-negative bacterial TonB protein / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal
Similarity search - Domain/homology
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsWojnowska, M. / Walker, D. / Yelland, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the C-terminal domain of FusB, a TonB homologue
Authors: Wojnowska, M. / Walker, D. / Yelland, T.
History
DepositionMar 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein TonB
A: Protein TonB


Theoretical massNumber of molelcules
Total (without water)19,5642
Polymers19,5642
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer/dimer equilibrium in solution, mostly monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-3 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.661, 94.661, 58.246
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 3 - 87 / Label seq-ID: 2 - 86

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein Protein TonB


Mass: 9782.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Gene: RC98_15010 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A837DIX8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.9 Å3/Da / Density % sol: 68.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris pH 8.5, 8% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.08→47.53 Å / Num. obs: 18033 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Net I/σ(I): 36.1
Reflection shellResolution: 2.08→2.14 Å / Num. unique obs: 1406 / CC1/2: 0.899

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gsk

2gsk


Resolution: 2.08→47.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.236 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23958 887 4.9 %RANDOM
Rwork0.21167 ---
obs0.2131 17121 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.833 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---1.23 Å2
Refinement stepCycle: 1 / Resolution: 2.08→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 0 57 1416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131381
X-RAY DIFFRACTIONr_bond_other_d00.0171318
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.6461868
X-RAY DIFFRACTIONr_angle_other_deg1.2131.5933026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7675171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95420.11885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2615236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9771517
X-RAY DIFFRACTIONr_chiral_restr0.0520.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
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_it4.4784.492690
X-RAY DIFFRACTIONr_mcbond_other4.4784.49689
X-RAY DIFFRACTIONr_mcangle_it5.6046.717859
X-RAY DIFFRACTIONr_mcangle_other5.6016.72860
X-RAY DIFFRACTIONr_scbond_it6.2545.255691
X-RAY DIFFRACTIONr_scbond_other6.2515.248689
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.1017.581009
X-RAY DIFFRACTIONr_long_range_B_refined11.28851.1711404
X-RAY DIFFRACTIONr_long_range_B_other11.28451.2081405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2274 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 73 -
Rwork0.254 1259 -
obs--100 %
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)
11.34541.5741-0.49871.948-0.31580.88960.08690.04860.14170.0982-0.00740.1368-0.0269-0.1973-0.07950.0661-0.045-0.00940.09720.00270.150821.0517-12.2969-4.6779
21.971.699-0.39451.59090.05441.92630.2153-0.16120.15570.07750.01210.1642-0.36320.5541-0.22740.1406-0.16550.01970.2134-0.03920.177347.46536.7687-8.6428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 88
2X-RAY DIFFRACTION2A2 - 88

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