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- PDB-1ihr: Crystal structure of the dimeric C-terminal domain of TonB -

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Basic information

Entry
Database: PDB / ID: 1ihr
TitleCrystal structure of the dimeric C-terminal domain of TonB
ComponentsTonB protein
KeywordsPROTEIN TRANSPORT / novel fold / intertwined dimer
Function / homology
Function and homology information


receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / siderophore transport / cell envelope / cobalamin 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 / siderophore transport / cell envelope / cobalamin 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 / : / Gram-negative bacterial TonB protein / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal ...TolA/TonB C-terminal domain / TonB / : / TonB polyproline region / : / Gram-negative bacterial TonB protein / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Protein TonB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsChang, C. / Mooser, A. / Pluckthun, A. / Wlodawer, A.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of the dimeric C-terminal domain of TonB reveals a novel fold.
Authors: Chang, C. / Mooser, A. / Pluckthun, A. / Wlodawer, A.
History
DepositionApr 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TonB protein
B: TonB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4476
Polymers17,1282
Non-polymers3204
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-40 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.770, 86.330, 26.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-336-

HOH

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Components

#1: Protein TonB protein


Mass: 8563.893 Da / Num. of mol.: 2 / Fragment: C-terminal domain residues 164-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: JM83 / Plasmid: pAT37 / Production host: Escherichia coli (E. coli) / Strain (production host): XLI-Blue / References: UniProt: P02929
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.89 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, Tris, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris1drop
215 mg/mlprotein1drop
328-30 %PEG33501reservoir
40.1 MTris1reservoir
550-100 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9800, 0.9163, 0.9196, 0.9199
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2000 / Details: FOCUSSING MIRROR
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.91631
30.91961
40.91991
ReflectionResolution: 1.55→30 Å / Num. all: 22232 / Num. obs: 21518 / % possible obs: 96.8 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 6.5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 40.5
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.8 / Num. unique all: 1745 / % possible all: 80.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 138987
Reflection shell
*PLUS
% possible obs: 80.2 % / Rmerge(I) obs: 0.11

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Processing

Software
NameClassification
SOLVEphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.55→20 Å / Num. parameters: 12576 / Num. restraintsaints: 14847 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1076 5.3 %RANDOM
Rwork0.1599 ---
all0.1657 20365 --
obs0.1657 20365 92.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeLuzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 20 Å / Num. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1384.5
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 4 219 1397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0236
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.067
X-RAY DIFFRACTIONs_approx_iso_adps0.079
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor obs: 0.16 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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