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- PDB-6pnv: 1.42 Angstrom Resolution Crystal Structure of Translocation Prote... -

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Basic information

Entry
Database: PDB / ID: 6pnv
Title1.42 Angstrom Resolution Crystal Structure of Translocation Protein TolB from Salmonella enterica
ComponentsTol-Pal system protein TolB
KeywordsTRANSLOCASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / translocation protein TolB.
Function / homology
Function and homology information


protein import / periplasmic space / cell cycle / cell division
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 ...: / 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
: / Tol-Pal system protein TolB / Tol-Pal system protein TolB
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.42 Angstrom Resolution Crystal Structure of Translocation Protein TolB from Salmonella enterica
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Tol-Pal system protein TolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0353
Polymers43,9731
Non-polymers622
Water8,269459
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-8 kcal/mol
Surface area17710 Å2
Unit cell
Length a, b, c (Å)63.894, 40.570, 77.994
Angle α, β, γ (deg.)90.000, 111.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tol-Pal system protein TolB


Mass: 43972.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2-4 / Variant: enterica / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): Gold(DE3) / References: UniProt: A0A0D6H0D6, UniProt: Q8ZQT5*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 5.2 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (G4), 0.2 M Potassium thiocyanate, 0.1 M Bis Tris propane pH 7.5, 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2019 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.42→30 Å / Num. obs: 67628 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.029 / Rrim(I) all: 0.062 / Rsym value: 0.054 / Χ2: 1.039 / Net I/σ(I): 22.8
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3512 / CC1/2: 0.709 / Rpim(I) all: 0.368 / Rrim(I) all: 0.726 / Rsym value: 0.622 / Χ2: 1.034 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w8b

2w8b


Resolution: 1.42→29.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.719 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.069
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3474 5.1 %RANDOM
Rwork0.1618 ---
obs0.1635 64124 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56.78 Å2 / Biso mean: 16.254 Å2 / Biso min: 6.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å2-0.7 Å2
2---0.29 Å20 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.42→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 2 477 3580
Biso mean--23.35 25.99 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133334
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173003
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.6464579
X-RAY DIFFRACTIONr_angle_other_deg0.4091.5727017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5125454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.7522.573171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.77415522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7711522
X-RAY DIFFRACTIONr_chiral_restr0.0650.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.023900
X-RAY DIFFRACTIONr_gen_planes_other0.0490.02698
X-RAY DIFFRACTIONr_rigid_bond_restr0.98336337
LS refinement shellResolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 221 -
Rwork0.267 4687 -
all-4908 -
obs--94.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72840.45660.00421.4464-0.14870.47250.011-0.0222-0.06970.0722-0.01340.0701-0.043-0.05230.00230.01030.00710.00950.0232-0.00970.0425-25.9666-2.5011-12.0874
20.68690.13740.0231.04190.52761.38370.0144-0.13530.04890.0190.0288-0.0615-0.04920.1646-0.04320.0041-0.00830.00040.0504-0.01260.0119-0.774115.7498-8.9902
30.68890.22760.13791.68910.36992.94210.004-0.04370.0055-0.09980.0403-0.2071-0.08560.4286-0.04430.01340.00420.01890.1374-0.01270.07989.876813.515-18.9907
41.2099-0.47650.73162.1025-0.53981.43230.01290.18740.0692-0.2322-0.0893-0.11690.00910.2580.07650.06320.01430.03990.09220.01830.0354.055716.0668-33.0393
50.9198-0.257-0.08521.06020.1420.54870.0380.0760.0567-0.0889-0.03480.0513-0.0372-0.0488-0.00320.01350.01220.00280.01950.01030.0158-13.04718.0818-22.9279
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 167
2X-RAY DIFFRACTION2A168 - 224
3X-RAY DIFFRACTION3A225 - 267
4X-RAY DIFFRACTION4A268 - 345
5X-RAY DIFFRACTION5A346 - 431

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