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- PDB-4xoa: Crystal structure of a FimH*DsG complex from E.coli K12 in space ... -

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Basic information

Entry
Database: PDB / ID: 4xoa
TitleCrystal structure of a FimH*DsG complex from E.coli K12 in space group P1
Components
  • FimG
  • Protein FimH
KeywordsCELL ADHESION / type I pilus / catch-bond / lectin / UPEC / bacterial adhesin / UTI / mannose / isomerase
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / mannose binding / host cell membrane / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Protein FimG / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.541 Å
AuthorsJakob, R.P. / Eras, J. / Glockshuber, R. / Maier, T.
CitationJournal: Nat Commun / Year: 2016
Title: Catch-bond mechanism of the bacterial adhesin FimH.
Authors: Sauer, M.M. / Jakob, R.P. / Eras, J. / Baday, S. / Eris, D. / Navarra, G. / Berneche, S. / Ernst, B. / Maier, T. / Glockshuber, R.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jan 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: FimG
H: FimG
A: Protein FimH
D: FimG
C: Protein FimH
F: FimG
E: Protein FimH
G: Protein FimH


Theoretical massNumber of molelcules
Total (without water)121,9928
Polymers121,9928
Non-polymers00
Water3,423190
1
B: FimG
A: Protein FimH


Theoretical massNumber of molelcules
Total (without water)30,4982
Polymers30,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-11 kcal/mol
Surface area13000 Å2
MethodPISA
2
H: FimG
G: Protein FimH


Theoretical massNumber of molelcules
Total (without water)30,4982
Polymers30,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-11 kcal/mol
Surface area13160 Å2
MethodPISA
3
D: FimG
C: Protein FimH


Theoretical massNumber of molelcules
Total (without water)30,4982
Polymers30,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-10 kcal/mol
Surface area13040 Å2
MethodPISA
4
F: FimG
E: Protein FimH


Theoretical massNumber of molelcules
Total (without water)30,4982
Polymers30,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-10 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.530, 77.624, 78.107
Angle α, β, γ (deg.)101.54, 111.13, 96.29
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
FimG


Mass: 1416.661 Da / Num. of mol.: 4 / Fragment: UNP residues 24-37
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimG / Plasmid: pTRC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: C4ZT07, UniProt: P08190*PLUS
#2: Protein
Protein FimH


Mass: 29081.314 Da / Num. of mol.: 4 / Fragment: UNP residues 22-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimH, b4320, JW4283 / Plasmid: pTRC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P08191
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2M Na Malonate, 20%PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.541→52.674 Å / Num. obs: 35539 / % possible obs: 90.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.8
Reflection shellResolution: 2.541→2.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2 / Num. unique all: 5844

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1779)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mcy, 1qun
Resolution: 2.541→52.674 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 1999 5.62 %Random selection
Rwork0.2398 ---
obs0.2409 35539 90.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.541→52.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8558 0 0 190 8748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048742
X-RAY DIFFRACTIONf_angle_d0.95512002
X-RAY DIFFRACTIONf_dihedral_angle_d12.5522974
X-RAY DIFFRACTIONf_chiral_restr0.0361454
X-RAY DIFFRACTIONf_plane_restr0.0041558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5409-2.60440.36341390.32262342X-RAY DIFFRACTION87
2.6044-2.67480.36341490.34792500X-RAY DIFFRACTION95
2.6748-2.75350.34671490.31452489X-RAY DIFFRACTION95
2.7535-2.84240.31861510.29652532X-RAY DIFFRACTION95
2.8424-2.9440.29041500.27452518X-RAY DIFFRACTION96
2.944-3.06180.30831500.28022517X-RAY DIFFRACTION96
3.0618-3.20120.27911500.26792537X-RAY DIFFRACTION96
3.2012-3.36990.29681520.25642544X-RAY DIFFRACTION95
3.3699-3.5810.28721430.26732406X-RAY DIFFRACTION92
3.581-3.85740.2982870.27811448X-RAY DIFFRACTION55
3.8574-4.24550.22961190.20612015X-RAY DIFFRACTION77
4.2455-4.85940.19431550.172579X-RAY DIFFRACTION97
4.8594-6.12090.19561510.16572542X-RAY DIFFRACTION97
6.1209-52.68530.19961540.18392571X-RAY DIFFRACTION97
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.33030.964-1.38455.9214-3.93155.1537-0.02970.06030.0001-0.1799-0.1081-0.29490.03120.18980.17590.1339-0.08490.11870.68840.06820.39-6.132922.184639.3223
23.955-0.56760.66788.022-4.64924.1983-0.1020.00980.10940.03670.0580.0593-0.1492-0.0647-0.00930.09510.0696-0.13450.56760.17380.3108-20.019215.6736-22.8665
31.74050.5193-1.8581.1888-0.35943.0195-0.21820.2597-0.3184-0.1654-0.0004-0.11750.2238-0.01360.26120.3156-0.0739-0.03370.7560.22430.363210.100533.87357.0835
41.89841.2907-2.29120.8597-1.65423.6912-0.12430.2097-0.0526-0.1089-0.1611-0.1045-0.09890.05480.04590.2684-0.0844-0.02670.84370.23840.360316.084340.62823.9468
50.9104-0.3041-0.39780.936-0.39741.77730.08610.0045-0.006-0.0499-0.083-0.0543-0.01340.0771-0.05450.2447-0.0461-0.02570.79950.16240.28776.870944.98494.1377
60.68430.2483-0.92040.2089-0.34641.5816-0.11820.0153-0.04340.01940.094-0.02520.1261-0.12330.00930.2355-0.0035-0.02770.8010.19320.35073.504538.18737.8816
70.6530.0427-0.05180.7934-0.43491.16670.01260.0712-0.1737-00.00320.0236-0.0459-0.1481-0.01420.22620.0052-0.07890.93990.32070.124-8.565729.617741.6182
83.62310.10220.31372.23853.10617.18310.02910.07890.0444-0.19760.01330.069-0.1347-0.17730.01210.1238-0.08930.02050.57390.10510.4494-28.4846-0.610133.096
92.66820.26671.6473.1891-1.57831.9787-0.29130.17490.4498-0.05270.09740.1253-0.5785-0.22230.19210.47510.0222-0.0481.10520.14380.4864-48.931310.5488-5.7287
100.8259-0.40860.6560.3035-0.37141.2878-0.0915-0.00720.2929-0.0576-0.04890.0812-0.0166-0.2055-0.01010.0923-0.12410.05531.05210.250.2704-43.9119-1.3134-6.2921
110.5007-0.12690.7910.162-0.48531.69850.12760.03930.21710.0790.17010.135-0.39510.18160.04930.19760.0132-0.11931.03050.37650.033-36.9089-0.01426.9237
120.89670.08620.32380.66210.14031.55160.02980.07030.0169-0.0105-0.0156-0.11510.07570.1052-0.01130.18760.00320.00280.66240.1730.2437-24.6494-8.849930.6568
132.3157-0.6374-2.661.48072.65626.6676-0.0001-0.0886-0.04210.14790.04070.03870.2702-0.2012-0.00670.1160.04780.02110.50830.22380.5018-6.8673-40.6824-14.6349
144.3632-0.3176-4.04742.27980.24023.7578-0.3125-0.092-0.4188-0.06940.13890.01430.5613-0.2340.17450.4217-0.11240.04331.05070.12610.5851-27.4024-51.593524.4062
150.63530.0072-0.46590.0906-0.46551.4593-0.0472-0.0507-0.1213-0.03790.05240.09730.1737-0.0827-0.01480.1422-0.03920.0120.87520.2050.3253-18.153-39.178417.1673
160.9698-0.1272-0.32780.42570.27271.320.04450.08-0.1508-0.05380.0649-0.094-0.00060.2353-0.06060.2062-0.0013-0.00060.71680.19780.2917-2.05-33.7123-14.6869
172.6383-1.12941.73942.39431.00192.7431-0.337-0.41430.20580.30820.0311-0.2553-0.49950.26550.35420.4379-0.0466-0.0370.98180.31520.46881.06443.997518.4176
180.5678-0.12440.77750.4985-0.23491.322-0.0145-0.1150.11140.01070.04180.0359-0.06010.1102-0.01610.20380.00050.00140.73140.17360.3483-5.2399-5.67411.6981
190.5893-0.31720.5227-0.0848-0.41421.0826-0.0193-0.1430.0014-0.10960.0468-0.1195-0.10210.09890.06080.1958-0.0411-0.03580.81910.24310.3053-9.687-1.98972.5908
200.8611-0.413-0.29871.3072-0.6491.14880.23770.11850.24590.03830.15620.07110.1947-0.1169-0.12250.1246-0.03450.16520.87190.37520.0476-24.08077.0075-24.9981
211.05880.1543-0.2891.0552-0.67431.5360.17790.07180.2191-0.08160.05690.2072-0.0592-0.1018-0.13490.10740.00250.00260.74220.19890.353-24.841910.3429-22.2429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 12 )
2X-RAY DIFFRACTION2chain 'H' and (resid 1 through 14 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 31 )
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 53 )
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 104 )
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 163 )
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 279 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 12 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 17 )
10X-RAY DIFFRACTION10chain 'C' and (resid 18 through 104 )
11X-RAY DIFFRACTION11chain 'C' and (resid 105 through 183 )
12X-RAY DIFFRACTION12chain 'C' and (resid 184 through 279 )
13X-RAY DIFFRACTION13chain 'F' and (resid 1 through 12 )
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 17 )
15X-RAY DIFFRACTION15chain 'E' and (resid 18 through 198 )
16X-RAY DIFFRACTION16chain 'E' and (resid 199 through 279 )
17X-RAY DIFFRACTION17chain 'G' and (resid 1 through 17 )
18X-RAY DIFFRACTION18chain 'G' and (resid 18 through 84 )
19X-RAY DIFFRACTION19chain 'G' and (resid 85 through 198 )
20X-RAY DIFFRACTION20chain 'G' and (resid 199 through 258 )
21X-RAY DIFFRACTION21chain 'G' and (resid 259 through 279 )

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