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- PDB-1c5k: THE STRUCTURE OF TOLB, AN ESSENTIAL COMPONENT OF THE TOL-DEPENDEN... -

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Basic information

Entry
Database: PDB / ID: 1c5k
TitleTHE STRUCTURE OF TOLB, AN ESSENTIAL COMPONENT OF THE TOL-DEPENDENT TRANSLOCATION SYSTEM AND ITS INTERACTIONS WITH THE TRANSLOCATION DOMAIN OF COLICIN E9
ComponentsPROTEIN (TOLB PROTEIN)
KeywordsTRANSPORT PROTEIN / BETA PROPELLOR / PROTEIN-PROTEIN INTERACTIONS / COLICIN IMPORT
Function / homology
Function and homology information


cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / protein import / cell division site / protein transport / outer membrane-bounded periplasmic space / periplasmic space / cell cycle / cell division ...cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / protein import / cell division site / 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
TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / WD40-like beta propeller / WD40-like Beta Propeller Repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase ...TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / WD40-like beta propeller / WD40-like Beta Propeller Repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
YTTERBIUM (III) ION / Tol-Pal system protein TolB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCarr, S. / Penfold, C.N. / Bamford, V. / James, R. / Hemmings, A.M.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9.
Authors: Carr, S. / Penfold, C.N. / Bamford, V. / James, R. / Hemmings, A.M.
History
DepositionDec 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: PROTEIN (TOLB PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3702
Polymers47,1971
Non-polymers1731
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.580, 40.190, 77.660
Angle α, β, γ (deg.)90.00, 110.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (TOLB PROTEIN)


Mass: 47196.594 Da / Num. of mol.: 1 / Fragment: ENTIRE PROTEIN
Source method: isolated from a genetically manipulated source
Details: IN E.COLI TOLB FORMS A HETERODIMER WITH PAL (PEPTIDOGLYCAN ASSOCIATED LIPOPROTEIN)
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PRJ379 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P0A855
#2: Chemical ChemComp-YB / YTTERBIUM (III) ION / Ytterbium


Mass: 173.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Yb
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.17 Å3/Da / Density % sol: 44 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
210 mMTris-HCl11
318 %(w/v)PEG800012
4100 mMMES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.91, 1.07, 1.386, 1.387
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 1, 1999 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911
21.071
31.3861
41.3871
ReflectionResolution: 1.9→20 Å / Num. obs: 59093 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 5.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.9 % / Rsym value: 17.6 / % possible all: 97.4
Reflection
*PLUS
Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.176

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2383 4.9 %RANDOM
Rwork0.234 ---
obs0.234 44970 97.3 %-
Displacement parametersBiso mean: 27.9 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 1 230 3222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.72
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.273 / Rfactor Rwork: 0.235

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