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- PDB-1qxx: CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF TONB -

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Basic information

Entry
Database: PDB / ID: 1qxx
TitleCRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF TONB
ComponentsTonB protein
KeywordsTRANSPORT PROTEIN / TonB Dimerization
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKoedding, J. / Howard, P. / Kaufmann, L. / Polzer, P. / Lustig, A. / Welte, W.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Dimerization of TonB is not essential for its binding to the outer membrane siderophore receptor FhuA of Escherichia coli.
Authors: Koedding, J. / Howard, P. / Kaufmann, L. / Polzer, P. / Lustig, A. / Welte, W.
History
DepositionSep 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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


Theoretical massNumber of molelcules
Total (without water)8,5641
Polymers8,5641
Non-polymers00
Water55831
1
A: TonB protein

A: TonB protein


Theoretical massNumber of molelcules
Total (without water)17,1282
Polymers17,1282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Buried area6230 Å2
ΔGint-41 kcal/mol
Surface area10360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.580, 61.580, 121.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsThe second part of the dimer is generated by symmetry operations in P6422

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Components

#1: Protein TonB protein


Mass: 8563.893 Da / Num. of mol.: 1 / Fragment: residues 164-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TONB / Plasmid: pET30a / 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 / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.89 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Sodium formiate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→26.44 Å / Num. all: 5019 / Num. obs: 4052 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.68 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 19.32
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.56 / Num. unique all: 409 / Rsym value: 0.463 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
MOLREPphasing
REFMAC5.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IHR

1ihr


Resolution: 2.7→26.44 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 202 -RANDOM
Rwork0.267 ---
all-5019 --
obs-4052 97.5 %-
Refinement stepCycle: LAST / Resolution: 2.7→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 0 31 632
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr.m.s. deviation bond length0.02
X-RAY DIFFRACTIONr.s.m. deviation bond angel1.72

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