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- PDB-1u07: Crystal Structure of the 92-residue C-term. part of TonB with sig... -

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Basic information

Entry
Database: PDB / ID: 1u07
TitleCrystal Structure of the 92-residue C-term. part of TonB with significant structural changes compared to shorter fragments
ComponentsTonB protein
KeywordsPROTEIN TRANSPORT / beta-hairpin
Function / homology
Function and homology information


receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / cell envelope / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex / cell outer membrane ...receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / cell envelope / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / protein domain specific binding / membrane / plasma membrane
Similarity search - Function
TolA/TonB C-terminal domain / TonB / : / TonB polyproline region / TonB C-terminal domain profile. / Gram-negative bacterial TonB protein / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.13 Å
AuthorsKoedding, J. / Killig, F. / Polzer, P. / Howard, S.P. / Diederichs, K. / Welte, W.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of a 92-residue c-terminal fragment of TonB from Escherichia coli reveals significant conformational changes compared to structures of smaller TonB fragments
Authors: Koedding, J. / Killig, F. / Polzer, P. / Howard, S.P. / Diederichs, K. / Welte, W.
History
DepositionJul 13, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 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

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Assembly

Deposited unit
A: TonB protein
B: TonB protein


Theoretical massNumber of molelcules
Total (without water)20,1852
Polymers20,1852
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-4 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.580, 49.320, 72.220
Angle α, β, γ (deg.)90.00, 97.99, 90.00
Int Tables number4
Space group name H-MP1211
Detailsputative dimer

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Components

#1: Protein TonB protein


Mass: 10092.567 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tonb / Plasmid: pTB92 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02929
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM imidazole, 1.1M sodium citrate, 100mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95372 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.08→10 Å / Num. all: 65348 / Num. obs: 65348 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.54 % / Biso Wilson estimate: 15.994 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.68
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 1.73 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.51 / Num. unique all: 2763 / % possible all: 78.5

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
SOLVEphasing
SHELXL-97refinement
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.13→10 Å / Num. parameters: 15000 / Num. restraintsaints: 18590 / Isotropic thermal model: anisotropic / Cross valid method: free R / σ(F): -3 / σ(I): -3
StereochEM target val spec case: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Stereochemistry target values: Engh & Huber
Details: structure was solved with MAD on a Seleno-Met crystal at 2A. This entry is based on the high resolution data measured at 0.95372A wavelength. Anisotropic scaling applied by the method of ...Details: structure was solved with MAD on a Seleno-Met crystal at 2A. This entry is based on the high resolution data measured at 0.95372A wavelength. Anisotropic scaling applied by the method of parkin, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2781 5 %RANDOM
Rwork0.137 ---
all0.139 55631 --
obs0.139 55631 99.9 %-
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 1445.46 / Occupancy sum non hydrogen: 1605.46
Refinement stepCycle: LAST / Resolution: 1.13→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 0 198 1662
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0269
X-RAY DIFFRACTIONs_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.066
X-RAY DIFFRACTIONs_approx_iso_adps0.113

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