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- PDB-4r40: Crystal Structure of TolB/Pal complex from Yersinia pestis. -

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Basic information

Entry
Database: PDB / ID: 4r40
TitleCrystal Structure of TolB/Pal complex from Yersinia pestis.
Components
  • Peptidoglycan-associated lipoprotein
  • Protein TolB
KeywordsPROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold and beta propeller fold / translocation and peptidoglycan-associated outer membrane lipoprotein
Function / homology
Function and homology information


protein import / cell outer membrane / periplasmic space / cell cycle / cell division
Similarity search - Function
Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / Outer membrane protein, OmpA-like, conserved site / WD40-like beta propeller / WD40-like Beta Propeller Repeat / OmpA-like domain. ...Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / Outer membrane protein, OmpA-like, conserved site / WD40-like beta propeller / WD40-like Beta Propeller Repeat / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / 60s Ribosomal Protein L30; Chain: A; / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Peptidoglycan-associated lipoprotein / Peptidoglycan-associated lipoprotein / Tol-Pal system protein TolB
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.496 Å
AuthorsMaltseva, N. / Kim, Y. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of TolB/Pal complex from Yersinia pestis.
Authors: Maltseva, N. / Kim, Y. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein TolB
B: Peptidoglycan-associated lipoprotein
C: Protein TolB
D: Peptidoglycan-associated lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95413
Polymers119,2024
Non-polymers7539
Water64936
1
A: Protein TolB
B: Peptidoglycan-associated lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0698
Polymers59,6012
Non-polymers4686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-41 kcal/mol
Surface area23040 Å2
MethodPISA
2
C: Protein TolB
D: Peptidoglycan-associated lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8855
Polymers59,6012
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-36 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.389, 175.252, 66.268
Angle α, β, γ (deg.)90.00, 89.83, 90.00
Int Tables number4
Space group name H-MP1211
Details2 heterodimers in the asymmetric unit

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Protein TolB


Mass: 44120.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: tolB, y3055, YPO1124, YP_1032 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q8ZGZ1
#2: Protein Peptidoglycan-associated lipoprotein / Peptidoglycan-associated lipoprotein Pal


Mass: 15480.468 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: excC, pal, y3054, YPO1125, YP_1031 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q7CH55, UniProt: A0A380PP88*PLUS

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Non-polymers , 4 types, 45 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M lithium sulfate monohydrate, 0.1M Bis-tris pH 7.5, 25% PEG 3550, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.496→43.821 Å / Num. all: 35354 / Num. obs: 35354 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 35.59 Å2 / Rsym value: 0.153 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 1499 / Rsym value: 0.448 / % possible all: 80.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1593)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4PWZ and 4PWT

4pwz

4pwt


Resolution: 2.496→43.821 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1593 5.23 %random
Rwork0.17 ---
all0.173 30433 --
obs0.173 30433 81.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.7 Å2
Refinement stepCycle: LAST / Resolution: 2.496→43.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8053 0 44 36 8133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078290
X-RAY DIFFRACTIONf_angle_d1.02711264
X-RAY DIFFRACTIONf_dihedral_angle_d15.0843010
X-RAY DIFFRACTIONf_chiral_restr0.0651233
X-RAY DIFFRACTIONf_plane_restr0.0061490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4976-2.57820.2983910.27931528161946
2.5782-2.67030.3404990.25821797189653
2.6703-2.77720.2772940.24462014210859
2.7772-2.90350.29061140.23332241235566
2.9035-3.05650.26661340.21992489262374
3.0565-3.24790.24071320.19672807293983
3.2479-3.49850.20881710.17243082325390
3.4985-3.85030.2181870.15873211339894
3.8503-4.40670.18831790.13033219339895
4.4067-5.54910.1521660.12453235340195
5.5491-37.60230.20131830.17283250343394
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)
12.34140.54460.70141.3548-0.90971.14230.08880.33460.29860.0732-0.0048-0.00290.52530.1321-0.11120.49450.09310.01160.2447-0.09270.488416.4929-27.4990.5743
21.5366-1.27350.63634.2071-3.8173.6950.1870.0834-0.11230.0585-0.0780.13850.067-0.0417-0.13770.2225-0.04860.04940.2095-0.10750.501611.6217-33.64445.2003
31.00151.6834-0.57352.8165-1.00881.3748-0.0343-0.0341-0.0993-0.27240.26320.0506-0.08380.02970.07090.17490.02790.05230.252-0.02880.52224.3464-24.0414.1065
40.29130.11190.13991.03260.38661.36580.00950.01440.0232-0.087-0.03360.1115-0.0279-0.12940.03440.19170.00630.01070.21360.01690.456913.36265.72469.6215
54.3161-0.9020.05522.61340.30940.9977-0.169-0.1677-0.17790.26970.2883-0.47010.3596-0.0417-0.05060.30420.015-0.02750.19180.01680.360222.6995-5.932515.833
63.7775-0.86080.47772.88910.4110.68850.2820.04470.0676-0.3422-0.2282-0.24740.0925-0.0307-0.03410.2860.02110.05820.19760.02450.366122.4851-7.15615.2362
70.98030.20271.02357.013-5.12769.07970.1867-0.1557-0.3102-0.7243-0.05840.39450.11690.789-0.09560.1203-0.00440.07970.3594-0.00150.572433.653430.4577-8.5882
86.6301-2.541-1.0778.0366-2.89593.77810.2244-0.5490.467-1.14260.0737-0.61260.22430.1716-0.29050.4289-0.03050.07420.1692-0.0460.472828.65433.5965-4.6612
90.02460.1316-0.03571.677-0.83861.66690.0680.013-0.2706-0.0123-0.1551-0.30450.0781-0.01210.06480.1534-0.0205-0.00180.31740.040.52328.099519.93722.3689
100.3796-0.1940.54971.27461.5933.70510.20660.06520.42220.06870.2162-0.22840.3073-0.1293-0.26080.1799-0.0990.08850.3043-0.02570.720516.284380.386132.8334
111.89710.9531.47252.06650.3612.1819-0.58880.14130.4989-0.58420.3001-0.1004-0.2021-0.09630.2320.4029-0.06180.03790.22530.01350.482115.928284.962427.8049
121.63390.63880.08393.7210.74831.1068-0.01920.0415-0.1503-0.4189-0.24420.5526-0.3318-0.27650.17440.3033-0.0401-0.00490.2833-0.03730.49415.863186.05628.5862
130.6262-0.43120.46283.5590.49970.52310.1106-0.0593-0.1209-0.0535-0.27850.3519-0.07010.08070.07410.1864-0.0640.06290.24060.03730.556211.029266.063331.1493
142.2148-2.26550.29284.97530.19410.4319-0.22070.31670.18040.36030.06350.1067-0.002-0.0114-0.03330.210.04180.06980.4289-0.05380.428913.689957.41338.6365
151.4147-1.68630.11722.5367-0.25480.029-0.30530.1667-0.30560.55130.33240.6707-0.0579-0.1052-0.11190.20080.00250.03540.35540.04310.58148.599545.339933.3847
160.43470.66270.33363.54040.62381.59420.0908-0.0953-0.0162-0.1267-0.11650.14380.1541-0.22780.02810.1898-0.02010.02630.234-0.00280.442911.759740.502216.3442
173.1298-0.146-0.61930.82650.12332.9898-0.103-0.056-0.0581-0.07230.1626-0.10920.2580.0062-0.07430.2550.0213-0.02780.1873-0.03650.576323.197357.247919.9795
181.99940.1957-1.03394.3379-5.20996.57090.0190.0943-0.3513-1.1197-0.241-0.2114-0.6843-0.08860.16810.76010.014-0.13590.2104-0.05830.601832.849716.453651.5579
192.96820.06711.4932.97-0.06024.1164-0.1460.3224-0.0272-0.17340.22390.24520.06550.1677-0.03760.39540.00090.06630.1413-0.09750.648535.236729.926829.0164
207.42486.8898-6.03116.6268-6.32568.26-0.7405-0.2956-0.60490.08010.2385-1.03970.42310.990.47780.52210.0612-0.11320.2513-0.03810.571738.838321.422833.8206
212.2105-1.77060.65297.52925.61246.67860.11830.1964-0.35130.6268-0.2652-0.44120.6323-0.44470.05790.421-0.00520.11030.22140.02640.375828.219314.48239.2426
223.24363.0953-0.99626.5561-2.22823.49460.07320.2689-0.3180.4960.10310.3378-0.15770.1085-0.1780.126-0.0082-0.00890.2083-0.01770.581425.404530.528134.2159
231.4657-0.17481.0884.2125-0.31522.8901-0.27680.18680.1579-0.20320.03760.5328-0.07050.22270.23180.2129-0.03580.01780.20120.00470.493127.585831.870630.3079
246.81820.877-1.31764.34420.10946.8885-0.0592-0.3572-0.28580.1573-0.05080.29390.19920.6960.34420.34950.0813-0.03530.2277-0.03470.462429.900231.145436.189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 362 )
5X-RAY DIFFRACTION5chain 'A' and (resid 363 through 389 )
6X-RAY DIFFRACTION6chain 'A' and (resid 390 through 430 )
7X-RAY DIFFRACTION7chain 'B' and (resid 45 through 76 )
8X-RAY DIFFRACTION8chain 'B' and (resid 77 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 168 )
10X-RAY DIFFRACTION10chain 'C' and (resid 23 through 53 )
11X-RAY DIFFRACTION11chain 'C' and (resid 54 through 87 )
12X-RAY DIFFRACTION12chain 'C' and (resid 88 through 138 )
13X-RAY DIFFRACTION13chain 'C' and (resid 139 through 179 )
14X-RAY DIFFRACTION14chain 'C' and (resid 180 through 198 )
15X-RAY DIFFRACTION15chain 'C' and (resid 199 through 240 )
16X-RAY DIFFRACTION16chain 'C' and (resid 241 through 328 )
17X-RAY DIFFRACTION17chain 'C' and (resid 329 through 429 )
18X-RAY DIFFRACTION18chain 'D' and (resid 45 through 62 )
19X-RAY DIFFRACTION19chain 'D' and (resid 63 through 76 )
20X-RAY DIFFRACTION20chain 'D' and (resid 77 through 83 )
21X-RAY DIFFRACTION21chain 'D' and (resid 84 through 92 )
22X-RAY DIFFRACTION22chain 'D' and (resid 93 through 109 )
23X-RAY DIFFRACTION23chain 'D' and (resid 110 through 160 )
24X-RAY DIFFRACTION24chain 'D' and (resid 161 through 168 )

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