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- PDB-1qun: X-RAY STRUCTURE OF THE FIMC-FIMH CHAPERONE ADHESIN COMPLEX FROM U... -

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Basic information

Entry
Database: PDB / ID: 1qun
TitleX-RAY STRUCTURE OF THE FIMC-FIMH CHAPERONE ADHESIN COMPLEX FROM UROPATHOGENIC E.COLI
Components
  • MANNOSE-SPECIFIC ADHESIN FIMH
  • PAPD-LIKE CHAPERONE FIMC
KeywordsCHAPERONE/STRUCTURAL PROTEIN / CHAPERONE ADHESIN DONOR STRAND COMPLEMENTATION / CHAPERONE-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / : / protein folding chaperone / cell wall organization ...pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion
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 / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Type 1 fimbrin D-mannose specific adhesin / Chaperone protein FimC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsChoudhury, D. / Thompson, A. / Stojanoff, V. / Langerman, S. / Pinkner, J. / Hultgren, S.J. / Knight, S.
CitationJournal: Science / Year: 1999
Title: X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli.
Authors: Choudhury, D. / Thompson, A. / Stojanoff, V. / Langermann, S. / Pinkner, J. / Hultgren, S.J. / Knight, S.D.
History
DepositionJul 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: PAPD-LIKE CHAPERONE FIMC
B: MANNOSE-SPECIFIC ADHESIN FIMH
C: PAPD-LIKE CHAPERONE FIMC
D: MANNOSE-SPECIFIC ADHESIN FIMH
E: PAPD-LIKE CHAPERONE FIMC
F: MANNOSE-SPECIFIC ADHESIN FIMH
G: PAPD-LIKE CHAPERONE FIMC
H: MANNOSE-SPECIFIC ADHESIN FIMH
I: PAPD-LIKE CHAPERONE FIMC
J: MANNOSE-SPECIFIC ADHESIN FIMH
K: PAPD-LIKE CHAPERONE FIMC
L: MANNOSE-SPECIFIC ADHESIN FIMH
M: PAPD-LIKE CHAPERONE FIMC
N: MANNOSE-SPECIFIC ADHESIN FIMH
O: PAPD-LIKE CHAPERONE FIMC
P: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)414,20316
Polymers414,20316
Non-polymers00
Water1,15364
1
A: PAPD-LIKE CHAPERONE FIMC
B: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-16 kcal/mol
Surface area21930 Å2
MethodPISA
2
C: PAPD-LIKE CHAPERONE FIMC
D: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-16 kcal/mol
Surface area21950 Å2
MethodPISA
3
E: PAPD-LIKE CHAPERONE FIMC
F: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-16 kcal/mol
Surface area21940 Å2
MethodPISA
4
G: PAPD-LIKE CHAPERONE FIMC
H: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-16 kcal/mol
Surface area21940 Å2
MethodPISA
5
I: PAPD-LIKE CHAPERONE FIMC
J: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-15 kcal/mol
Surface area22430 Å2
MethodPISA
6
K: PAPD-LIKE CHAPERONE FIMC
L: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-15 kcal/mol
Surface area22430 Å2
MethodPISA
7
M: PAPD-LIKE CHAPERONE FIMC
N: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-15 kcal/mol
Surface area22430 Å2
MethodPISA
8
O: PAPD-LIKE CHAPERONE FIMC
P: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-15 kcal/mol
Surface area22420 Å2
MethodPISA
9
E: PAPD-LIKE CHAPERONE FIMC
F: MANNOSE-SPECIFIC ADHESIN FIMH

E: PAPD-LIKE CHAPERONE FIMC
F: MANNOSE-SPECIFIC ADHESIN FIMH

M: PAPD-LIKE CHAPERONE FIMC
N: MANNOSE-SPECIFIC ADHESIN FIMH

M: PAPD-LIKE CHAPERONE FIMC
N: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)207,1018
Polymers207,1018
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_656-x+3/2,y+1/2,-z+11
Buried area19000 Å2
ΔGint-102 kcal/mol
Surface area82450 Å2
MethodPISA
10
A: PAPD-LIKE CHAPERONE FIMC
B: MANNOSE-SPECIFIC ADHESIN FIMH
O: PAPD-LIKE CHAPERONE FIMC
P: MANNOSE-SPECIFIC ADHESIN FIMH

G: PAPD-LIKE CHAPERONE FIMC
H: MANNOSE-SPECIFIC ADHESIN FIMH
K: PAPD-LIKE CHAPERONE FIMC
L: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)207,1018
Polymers207,1018
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1,-z+11
Buried area18980 Å2
ΔGint-101 kcal/mol
Surface area82480 Å2
MethodPISA
11
C: PAPD-LIKE CHAPERONE FIMC
D: MANNOSE-SPECIFIC ADHESIN FIMH

C: PAPD-LIKE CHAPERONE FIMC
D: MANNOSE-SPECIFIC ADHESIN FIMH

I: PAPD-LIKE CHAPERONE FIMC
J: MANNOSE-SPECIFIC ADHESIN FIMH

I: PAPD-LIKE CHAPERONE FIMC
J: MANNOSE-SPECIFIC ADHESIN FIMH


Theoretical massNumber of molelcules
Total (without water)207,1018
Polymers207,1018
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_547-x+1/2,y-1/2,-z+21
Buried area18810 Å2
ΔGint-101 kcal/mol
Surface area82660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.410, 139.570, 215.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
PAPD-LIKE CHAPERONE FIMC


Mass: 22694.023 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P31697
#2: Protein
MANNOSE-SPECIFIC ADHESIN FIMH


Mass: 29081.314 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P08191
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: Ammonium Sulphate, Tris, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlFimC-FimH1drop
2300 mMC-HEGA1drop
31 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoirpH8.2

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARRESEARCH / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 182983 / Num. obs: 142580 / Observed criterion σ(F): 2
Reflection
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Rmerge(I) obs: 0.253

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 7129 5 %RANDOM
Rwork0.24 ---
all-182983 --
obs-142580 --
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28800 0 0 64 28864
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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