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- PDB-1lr0: Pseudomonas aeruginosa TolA Domain III, Seleno-methionine Derivative -

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Basic information

Entry
Database: PDB / ID: 1lr0
TitlePseudomonas aeruginosa TolA Domain III, Seleno-methionine Derivative
ComponentsTolA protein
KeywordsPROTEIN TRANSPORT / Domain-Swapping / TolA / TonB
Function / homology
Function and homology information


bacteriocin transport / toxin transmembrane transporter activity / cell cycle / cell division / plasma membrane
Similarity search - Function
TonB C terminal / Tol-Pal system, TolA / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / TonB/TolA, C-terminal / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tol-Pal system protein TolA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.914 Å
AuthorsWitty, M. / Sanz, C. / Shah, A. / Grossman, J.G. / Mizuguchi, K. / Perham, R.N. / Luisi, B.
CitationJournal: EMBO J. / Year: 2002
Title: Structure of the periplasmic domain of Pseudomonas aeruginosa TolA: evidence for an evolutionary relationship with the TonB transporter protein.
Authors: Witty, M. / Sanz, C. / Shah, A. / Grossmann, J.G. / Mizuguchi, K. / Perham, R.N. / Luisi, B.
History
DepositionMay 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.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: TolA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8704
Polymers14,6171
Non-polymers2533
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TolA protein
hetero molecules

A: TolA protein
hetero molecules

A: TolA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,60912
Polymers43,8503
Non-polymers7599
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4300 Å2
ΔGint-257 kcal/mol
Surface area20350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.477, 78.477, 97.674
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

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Components

#1: Protein TolA protein


Mass: 14616.770 Da / Num. of mol.: 1 / Fragment: Periplasmic Domain (residues 226-347)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: TOLA / Plasmid: pET-11c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P50600
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5% wt/v PEG 6000, 100 mM TrisCl, pH 8.0, and 1 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
30.05 %(w/v)octyl-glucoside1drop
45 %(w/v)PEG60001reservoir
5100 mMTris-HCl1reservoirpH8.0
61 mM1reservoirZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9791, 0.9611
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2001
RadiationMonochromator: Double-crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.96111
ReflectionResolution: 1.914→19.84 Å / Num. all: 13441 / Num. obs: 13441 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 16.1
Reflection shellResolution: 1.914→2.01 Å / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.322 / % possible all: 94.3
Reflection
*PLUS
Highest resolution: 1.914 Å / Lowest resolution: 19.84 Å / Num. measured all: 263045 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Highest resolution: 1.94 Å / % possible obs: 94.3 % / Rmerge(I) obs: 0.322

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.914→19.84 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.797 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22275 664 4.9 %RANDOM
Rwork0.18124 ---
all0.18325 13441 --
obs0.18325 13441 95.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.39 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.914→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 10 122 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021993
X-RAY DIFFRACTIONr_bond_other_d0.0010.02910
X-RAY DIFFRACTIONr_angle_refined_deg2.1551.9551348
X-RAY DIFFRACTIONr_angle_other_deg0.98332111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8513125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58615175
X-RAY DIFFRACTIONr_chiral_restr0.1380.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021109
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02192
X-RAY DIFFRACTIONr_nbd_refined0.2630.3231
X-RAY DIFFRACTIONr_nbd_other0.2110.3862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.590
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0880.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3340.519
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0110.51
X-RAY DIFFRACTIONr_mcbond_it1.7251.5635
X-RAY DIFFRACTIONr_mcangle_it2.99921024
X-RAY DIFFRACTIONr_scbond_it4.813358
X-RAY DIFFRACTIONr_scangle_it7.7274.5324
LS refinement shellResolution: 1.914→1.964 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.374 24
Rwork0.236 294
Refinement
*PLUS
Highest resolution: 1.914 Å / Lowest resolution: 19.84 Å / Num. reflection obs: 12777 / % reflection Rfree: 5 % / Rfactor obs: 0.181 / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.024
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.06
X-RAY DIFFRACTIONr_plane_restr0.017
X-RAY DIFFRACTIONr_chiral_restr0.128

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