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- PDB-5by4: Structure and function of the Escherichia coli Tol-Pal stator pro... -

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Basic information

Entry
Database: PDB / ID: 5by4
TitleStructure and function of the Escherichia coli Tol-Pal stator protein TolR
ComponentsProtein TolR
KeywordsPROTEIN TRANSPORT / strand-swapped dimer
Function / homology
Function and homology information


regulation of membrane invagination / bacteriocin transport / cell division site / transmembrane transporter activity / protein transport / cell cycle / cell division / membrane / plasma membrane
Similarity search - Function
Tol-Pal system protein TolR / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR
Similarity search - Domain/homology
Tol-Pal system protein TolR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsWojdyla, J.A. / Kaminska, R. / Kleanthous, C.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure and Function of the Escherichia coli Tol-Pal Stator Protein TolR.
Authors: Wojdyla, J.A. / Cutts, E. / Kaminska, R. / Papadakos, G. / Hopper, J.T. / Stansfeld, P.J. / Staunton, D. / Robinson, C.V. / Kleanthous, C.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein TolR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7744
Polymers11,7051
Non-polymers693
Water2,900161
1
A: Protein TolR
hetero molecules

A: Protein TolR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5498
Polymers23,4112
Non-polymers1386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4320 Å2
ΔGint-84 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.727, 51.727, 155.029
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-334-

HOH

31A-411-

HOH

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Components

#1: Protein Protein TolR


Mass: 11705.334 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 36-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tolR, b0738, JW0728 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABV6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes buffer pH 7.5, 1.0 M sodium phosphate and 0.8 M potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 25551 / Num. obs: 25522 / % possible obs: 99.9 % / Redundancy: 23 % / Net I/σ(I): 27
Reflection shellResolution: 1.7→1.8 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JWK and 2PFU

2jwk

2pfu


Resolution: 1.702→20 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 716 5.01 %
Rwork0.1751 --
obs0.177 14354 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.702→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms788 0 3 161 952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007897
X-RAY DIFFRACTIONf_angle_d1.1641237
X-RAY DIFFRACTIONf_dihedral_angle_d13.5352
X-RAY DIFFRACTIONf_chiral_restr0.083148
X-RAY DIFFRACTIONf_plane_restr0.005168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7021-1.83350.2351300.20342641X-RAY DIFFRACTION100
1.8335-2.0180.23651600.18042619X-RAY DIFFRACTION100
2.018-2.310.191420.15712661X-RAY DIFFRACTION100
2.31-2.91020.23651380.18372730X-RAY DIFFRACTION100
2.9102-38.79580.20551460.17192917X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.0743 Å / Origin y: 10.7285 Å / Origin z: 2.7295 Å
111213212223313233
T0.1207 Å2-0.0013 Å20.0016 Å2-0.0784 Å2-0.0002 Å2--0.0949 Å2
L0.3952 °20.171 °20.2716 °2-1.0219 °20.0461 °2--0.6992 °2
S-0.0118 Å °-0.0015 Å °0.0153 Å °0.0446 Å °-0.0376 Å °-0.0075 Å °-0.1262 Å °0.001 Å °-0.005 Å °
Refinement TLS groupSelection details: all

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