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- PDB-6swh: Crystal structure of the ternary complex between the type 1 pilus... -

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Basic information

Entry
Database: PDB / ID: 6swh
TitleCrystal structure of the ternary complex between the type 1 pilus proteins FimC, FimI and FimA from E. coli
Components
  • Chaperone protein FimC
  • Fimbrin-like protein FimI
  • Type-1 fimbrial protein, A chain
KeywordsSTRUCTURAL PROTEIN / structural protein complex / pilus assembly inhibition
Function / homology
Function and homology information


pilus assembly / cell adhesion involved in single-species biofilm formation / pilus / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / identical protein binding
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Type-1 fimbrial protein, A chain / Chaperone protein FimC / Fimbrin-like protein FimI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGiese, C. / Puorger, C. / Ignatov, O. / Weber, M. / Scharer, M.A. / Capitani, G. / Glockshuber, R.
Funding support1items
OrganizationGrant numberCountry
Swiss National Science Foundation
CitationJournal: To Be Published
Title: Comprehensive kinetic characterization of bacterial pilus rod assembly and assembly termination
Authors: Giese, C. / Puorger, C. / Ignatov, O. / Weber, M. / Scharer, M.A. / Capitani, G. / Glockshuber, R.
History
DepositionSep 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Derived calculations
Category: pdbx_struct_sheet_hbond / struct_sheet ...pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Revision 1.2Jan 24, 2024Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein FimC
B: Fimbrin-like protein FimI
C: Type-1 fimbrial protein, A chain
D: Chaperone protein FimC
E: Fimbrin-like protein FimI
F: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0738
Polymers110,9046
Non-polymers1682
Water2,936163
1
A: Chaperone protein FimC
B: Fimbrin-like protein FimI
C: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6205
Polymers55,4523
Non-polymers1682
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-18 kcal/mol
Surface area20970 Å2
MethodPISA
2
D: Chaperone protein FimC
E: Fimbrin-like protein FimI
F: Type-1 fimbrial protein, A chain


Theoretical massNumber of molelcules
Total (without water)55,4523
Polymers55,4523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-27 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.350, 198.350, 87.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Chaperone protein FimC


Mass: 22754.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimC, b4316, JW4279 / Production host: Escherichia coli (E. coli) / References: UniProt: P31697
#2: Protein Fimbrin-like protein FimI


Mass: 17189.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimI, b4315, JW5779 / Production host: Escherichia coli (E. coli) / References: UniProt: P39264
#3: Protein Type-1 fimbrial protein, A chain / Type-1A pilin


Mass: 15508.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimA, pilA, b4314, JW4277 / Production host: Escherichia coli (E. coli) / References: UniProt: P04128

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Non-polymers , 3 types, 165 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 4.46 Å3/Da / Density % sol: 72.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.8 M sodium formate, 100 mM Tris/acetic acid pH 8.5, 16% PEG 4000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→22 Å / Num. obs: 48258 / % possible obs: 99.3 % / Redundancy: 5.851 % / Biso Wilson estimate: 63.2 Å2 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Χ2: 0.991 / Net I/σ(I): 21.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2.8-35.1370.5763.0789450.64399.2
3-45.7840.12813.02226110.14199.4
4-66.360.04138.38117530.04599.9
6-106.2780.02948.1539350.03299.9
10-126.2060.02363.94670.02599.8
12-156.0410.02262.83160.02499.4
15-1860.02362.471420.025100
18-195.5710.02259.94280.025100
19-205.6960.02761.94230.029100
20-215.40.02463.13200.026100
21-225.50.02463.06180.02713.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15rc3_3435refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SQB

3sqb


Resolution: 2.8→19.891 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.59
RfactorNum. reflection% reflection
Rfree0.207 1010 2.09 %
Rwork0.1705 --
obs0.1713 48217 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 218.28 Å2 / Biso mean: 80.5496 Å2 / Biso min: 29.51 Å2
Refinement stepCycle: final / Resolution: 2.8→19.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7206 0 11 163 7380
Biso mean--83.56 62.84 -
Num. residues----961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.94720.31511430.2626666099
2.9472-3.13120.27921430.2337667699
3.1312-3.37190.27971430.2088670699
3.3719-3.70930.2161440.17886706100
3.7093-4.24150.18871440.15536771100
4.2415-5.32680.15991450.13216779100
5.3268-19.8910.19281480.16176909100
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)
14.28821.662-0.08518.33550.18683.43880.3473-0.2889-0.1587-0.14770.1298-0.6199-0.40391.1623-0.44720.8840.0913-0.05810.5189-0.17460.526-80.1120.8017-5.5471
28.16951.0161-0.45888.2267-1.33116.5435-0.1349-0.0657-0.2278-0.90141.3704-0.3904-0.54990.6571-1.06051.01620.0725-0.04850.728-0.330.5978-74.59436.6858-4.9712
33.1484-1.1627-0.46113.08151.60211.37640.0206-0.22870.0211-0.24380.4204-0.75830.03710.4497-0.39650.91040.075-0.13230.5715-0.11750.4055-82.1273.9354-2.0284
44.32021.54882.03482.60861.10862.58620.2387-0.4301-0.63580.15660.0155-0.35730.5823-0.4723-0.19521.08840.0861-0.0860.43130.05410.4167-98.205-15.8295-8.381
53.0621-3.4256-4.77788.50435.17438.3135-0.6938-0.6664-0.42210.73070.7836-0.76560.52841.4343-0.03220.78270.10290.01930.6417-0.26950.7367-78.7516-7.6036-24.8027
62.1010.84730.64353.93725.56539.11630.3364-0.02550.3314-1.366-0.8555-0.5665-1.56480.2840.49910.94450.01770.0510.4892-0.04120.5885-89.666816.7723-10.5842
77.037-4.7809-6.54384.20515.74798.79770.76490.32510.8405-0.1550.087-0.0863-0.6985-0.6377-0.99910.92220.139-0.00090.39840.12920.5317-104.552727.16485.7979
83.1351-2.9513-3.14076.66336.10495.59410.2770.55350.0411-1.0495-0.242-0.27530.02130.28660.02250.95580.0509-0.07980.3529-0.01290.4126-96.11687.3706-10.3593
98.27733.8491-1.63784.9387-3.57123.7373-0.0286-0.6678-0.38170.4474-0.09180.05960.4926-0.40380.20450.88510.0194-0.03960.36670.00430.3379-99.53414.311112.6924
107.89946.16311.81776.53894.29075.1652-0.0806-0.37730.42990.05150.3421-0.1145-0.18380.1437-0.38260.807-0.0033-0.12930.28990.00560.3962-94.515524.317313.9463
114.8497-0.2494-2.3890.05520.15571.13070.23260.5789-0.4915-0.55720.09170.15981.0931-0.4377-0.21341.0656-0.0292-0.16770.34140.00420.3548-103.332411.98-1.5471
123.52444.9602-2.72578.2764-3.74385.76170.1952-0.35930.92880.73960.24930.0746-0.55450.2113-0.31290.64460.0735-0.14380.3931-0.05780.4437-98.482425.383412.3574
135.6547-3.1561-3.40374.10744.77586.14220.163-0.0925-0.14480.33930.01290.00850.64340.1768-0.16141.03470.156-0.13090.33670.00540.3636-92.11224.0148-3.8347
145.70642.9697-1.62333.852-3.50283.33580.2056-1.1748-1.0983-0.0691-0.2003-1.1391-0.34181.60480.1350.7443-0.0206-0.11490.8552-0.25180.9072-70.3991-9.2628-28.009
156.02620.1279-0.71995.40143.09268.1225-0.35660.5007-0.2801-0.42120.6834-0.5946-0.37831.1635-0.28741.0261-0.2130.19040.5934-0.16050.5732-80.3718-5.8606-34.0638
167.9696-5.10073.53354.3089-4.30865.5277-0.27270.10151.8515-1.6468-0.8765-2.9728-0.94022.07910.89581.3638-0.50670.39461.1268-0.15371.413-72.7025-2.1148-43.3006
171.90312.19633.74193.0414.06197.5699-1.09790.8538-0.2422-0.19750.8936-0.6055-0.43541.66470.30391.307-0.64280.47251.6236-0.49121.1748-67.0887-5.2371-44.3431
181.50650.38961.84883.2471-0.2682.6636-0.3120.97310.2185-0.37050.3832-1.1397-0.380.99430.13571.0544-0.08210.25580.8867-0.2110.7244-76.8682-7.7723-35.1273
195.3085-0.37480.6248.61085.49099.2875-0.04730.00360.7533-0.3609-0.16520.5077-0.0858-0.17190.17440.612-0.1429-0.06540.3302-0.07790.6647-86.565843.876613.5737
208.42974.6375-1.10715.6772-0.08572.5358-0.89140.29690.5616-1.2310.53740.9159-0.02970.11390.36311.0525-0.164-0.19810.4991-0.04110.6236-87.445441.74985.9742
213.2799-1.5354-1.01593.14474.1254.72280.510.56192.2032-0.3638-0.9361.0711-1.3911-1.57661.63950.8614-0.3157-0.11330.6536-0.5341.4561-94.922150.38217.8391
223.5544-0.68891.45876.59461.64460.75270.22130.21030.2416-0.896-0.24270.00350.09990.1087-0.15570.8334-0.15120.1030.4806-0.05730.5204-80.165829.52310.6991
233.114-0.26430.5723.28663.28864.1390.2509-0.8270.5450.6418-0.78190.67770.3443-0.39110.37020.8456-0.3830.17890.5939-0.24130.8995-82.874950.598235.4946
243.88231.04931.22555.35333.43335.26240.3572-0.79020.0321.5147-0.470.57840.4393-0.47580.1231.2074-0.42640.17970.7601-0.12780.6909-78.036350.635339.1556
250.9625-1.4088-0.36163.3086-1.6913.50050.10080.36440.07710.8407-0.2743-0.277-0.07460.07640.26630.3735-0.1935-0.12360.6522-0.00750.5952-76.364663.785312.1779
264.697-1.1129-2.64564.0404-1.88243.22330.98681.1083-0.3373-3.0262-1.4535-1.37030.19031.30290.16080.99140.10620.14790.8849-0.21370.9834-70.252223.17219.6
275.05061.782-4.56237.93520.93577.9767-1.0073-1.1761-1.42320.6909-0.3469-3.83625.12053.68021.42631.9010.43280.08471.0370.22031.5634-72.55993.669919.1882
282.08711.03480.18718.24461.89243.64280.038-0.0352-0.30020.21080.0958-0.91740.47150.5163-0.15930.64150.045-0.08690.5163-0.11860.4566-76.29624.423919.4598
293.7531-1.59510.20674.0083-1.02882.51490.034-0.28160.18060.8621-0.1576-0.60180.41650.62670.10370.8417-0.0176-0.1120.5091-0.10780.4825-75.62222.741822.0495
302.62880.90281.20374.633-0.99342.94610.63660.4866-0.044-1.6392-0.01451.07880.5587-0.5864-0.56090.6115-0.2168-0.02460.89640.00290.5312-78.749274.10683.5916
310.0257-0.03790.27252.06322.33492.961-0.25610.82840.1493-0.06470.3277-0.4857-0.32410.5417-0.0860.5865-0.29060.02640.7149-0.03250.5262-66.804674.987510.4048
325.48580.65721.39264.5862-2.87668.34350.53160.08280.01560.3183-0.13460.3382-0.18310.0699-0.50990.5197-0.18580.05040.653-0.11840.4917-70.500269.218411.4352
337.2881-0.61145.18555.1949-0.07834.03060.48090.3222-0.0644-0.2257-0.4610.643-0.49480.31530.19680.8137-0.1069-0.06821.10.03880.6041-75.044982.9907-4.4599
343.2951-2.10840.90979.8505-2.69335.57760.17240.5896-0.0768-0.74030.13320.11370.0877-0.0883-0.28650.4794-0.2514-0.08820.6658-0.00970.4092-73.803672.41477.3716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 60 )A48 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 106 )A61 - 106
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 205 )A107 - 205
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 24 )B11 - 24
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 33 )B25 - 33
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 54 )B34 - 54
8X-RAY DIFFRACTION8chain 'B' and (resid 55 through 77 )B55 - 77
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 87 )B78 - 87
10X-RAY DIFFRACTION10chain 'B' and (resid 88 through 99 )B88 - 99
11X-RAY DIFFRACTION11chain 'B' and (resid 100 through 139 )B100 - 139
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 153 )B140 - 153
13X-RAY DIFFRACTION13chain 'B' and (resid 154 through 160 )B154 - 160
14X-RAY DIFFRACTION14chain 'C' and (resid 25 through 38 )C25 - 38
15X-RAY DIFFRACTION15chain 'C' and (resid 39 through 104 )C39 - 104
16X-RAY DIFFRACTION16chain 'C' and (resid 105 through 114 )C105 - 114
17X-RAY DIFFRACTION17chain 'C' and (resid 115 through 133 )C115 - 133
18X-RAY DIFFRACTION18chain 'C' and (resid 134 through 158 )C134 - 158
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 47 )D1 - 47
20X-RAY DIFFRACTION20chain 'D' and (resid 48 through 60 )D48 - 60
21X-RAY DIFFRACTION21chain 'D' and (resid 61 through 80 )D61 - 80
22X-RAY DIFFRACTION22chain 'D' and (resid 81 through 106 )D81 - 106
23X-RAY DIFFRACTION23chain 'D' and (resid 107 through 164 )D107 - 164
24X-RAY DIFFRACTION24chain 'D' and (resid 165 through 205 )D165 - 205
25X-RAY DIFFRACTION25chain 'E' and (resid 6 through 27 )E6 - 27
26X-RAY DIFFRACTION26chain 'E' and (resid 28 through 39 )E28 - 39
27X-RAY DIFFRACTION27chain 'E' and (resid 40 through 49 )E40 - 49
28X-RAY DIFFRACTION28chain 'E' and (resid 50 through 99 )E50 - 99
29X-RAY DIFFRACTION29chain 'E' and (resid 100 through 160 )E100 - 160
30X-RAY DIFFRACTION30chain 'F' and (resid 18 through 68 )F18 - 68
31X-RAY DIFFRACTION31chain 'F' and (resid 69 through 84 )F69 - 84
32X-RAY DIFFRACTION32chain 'F' and (resid 85 through 114 )F85 - 114
33X-RAY DIFFRACTION33chain 'F' and (resid 115 through 128 )F115 - 128
34X-RAY DIFFRACTION34chain 'F' and (resid 129 through 159 )F129 - 159

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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