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- PDB-3rfz: Crystal structure of the FimD usher bound to its cognate FimC:Fim... -

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Basic information

Entry
Database: PDB / ID: 3rfz
TitleCrystal structure of the FimD usher bound to its cognate FimC:FimH substrate
Components
  • Chaperone protein fimC
  • Outer membrane usher protein, type 1 fimbrial synthesis
  • Type 1 fimbrial adhesin
KeywordsCELL ADHESION/TRANSPORT/CHAPERONE / beta-barrel / pilus assembly / outer-membrane / CELL ADHESION-TRANSPORT PROTEIN-CHAPERONE complex / CELL ADHESION-TRANSPORT-CHAPERONE complex
Function / homology
Function and homology information


pilus organization / fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane ...pilus organization / fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / chaperone-mediated protein folding / protein folding chaperone / cell wall organization / cell outer membrane / outer membrane-bounded periplasmic space / cell adhesion
Similarity search - Function
Outer membrane usher protein FimD, plug domain / Outer membrane usher protein / PapC, C-terminal domain / PapC, N-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily ...Outer membrane usher protein FimD, plug domain / Outer membrane usher protein / PapC, C-terminal domain / PapC, N-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / 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 / 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 / Ubiquitin-like (UB roll) / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Type 1 fimbrin D-mannose specific adhesin / Outer membrane usher protein FimD / Chaperone protein FimC / Chaperone protein FimC / Type 1 fimbrial adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPhan, G. / Remaut, H. / Lebedev, A. / Geibel, S. / Waksman, G.
CitationJournal: Nature / Year: 2011
Title: Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate.
Authors: Phan, G. / Remaut, H. / Wang, T. / Allen, W.J. / Pirker, K.F. / Lebedev, A. / Henderson, N.S. / Geibel, S. / Volkan, E. / Yan, J. / Kunze, M.B. / Pinkner, J.S. / Ford, B. / Kay, C.W. / Li, H. ...Authors: Phan, G. / Remaut, H. / Wang, T. / Allen, W.J. / Pirker, K.F. / Lebedev, A. / Henderson, N.S. / Geibel, S. / Volkan, E. / Yan, J. / Kunze, M.B. / Pinkner, J.S. / Ford, B. / Kay, C.W. / Li, H. / Hultgren, S.J. / Thanassi, D.G. / Waksman, G.
History
DepositionApr 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 1 fimbrial adhesin
B: Outer membrane usher protein, type 1 fimbrial synthesis
C: Chaperone protein fimC
D: Type 1 fimbrial adhesin
E: Outer membrane usher protein, type 1 fimbrial synthesis
F: Chaperone protein fimC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,8758
Polymers290,6836
Non-polymers1922
Water73941
1
A: Type 1 fimbrial adhesin
B: Outer membrane usher protein, type 1 fimbrial synthesis
C: Chaperone protein fimC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,5345
Polymers145,3423
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-42 kcal/mol
Surface area54100 Å2
MethodPISA
2
D: Type 1 fimbrial adhesin
E: Outer membrane usher protein, type 1 fimbrial synthesis
F: Chaperone protein fimC


Theoretical massNumber of molelcules
Total (without water)145,3423
Polymers145,3423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11300 Å2
ΔGint-33 kcal/mol
Surface area54970 Å2
MethodPISA
3
A: Type 1 fimbrial adhesin
B: Outer membrane usher protein, type 1 fimbrial synthesis
C: Chaperone protein fimC
hetero molecules

D: Type 1 fimbrial adhesin
E: Outer membrane usher protein, type 1 fimbrial synthesis
F: Chaperone protein fimC


Theoretical massNumber of molelcules
Total (without water)290,8758
Polymers290,6836
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area23880 Å2
ΔGint-90 kcal/mol
Surface area107740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.190, 95.900, 144.570
Angle α, β, γ (deg.)90.00, 112.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 279
2115D1 - 279
1125B28 - 834
2125E28 - 834
1135C1 - 205
2135F1 - 205

NCS ensembles :
ID
1
2
3
DetailsFimD:FimC:FimH

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Components

#1: Protein Type 1 fimbrial adhesin


Mass: 29178.436 Da / Num. of mol.: 2 / Fragment: unp residues 22-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b4320, fimH, JW4283 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5D223, UniProt: P08191*PLUS
#2: Protein Outer membrane usher protein, type 1 fimbrial synthesis


Mass: 92640.227 Da / Num. of mol.: 2 / Fragment: unp residues 46-878
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimD, ECB_04186 / Production host: Escherichia coli (E. coli) / References: UniProt: C6UL88, UniProt: P30130*PLUS
#3: Protein Chaperone protein fimC /


Mass: 23522.906 Da / Num. of mol.: 2 / Fragment: unp residues 37-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimC, c5395 / Production host: Escherichia coli (E. coli) / References: UniProt: P59590, UniProt: P31697*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, ammonium acetate, isopropanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2009
RadiationMonochromator: tunable undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.8→59.13 Å / Num. obs: 76954 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 8
Reflection shellResolution: 2.8→2.95 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0077refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→59.13 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.881 / SU B: 17.593 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28181 3845 5 %RANDOM
Rwork0.22274 ---
obs0.22574 73065 97.32 %-
all-117208 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.16 Å2
2---0.24 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.8→59.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19068 0 10 41 19119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02219486
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.94526600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93152502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60124.583875
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.603152911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.50515104
X-RAY DIFFRACTIONr_chiral_restr0.0690.23006
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115082
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1116MEDIUM POSITIONAL0.230.5
1A905LOOSE POSITIONAL0.335
1A1116MEDIUM THERMAL5.292
1A905LOOSE THERMAL4.7310
2B3100MEDIUM POSITIONAL0.360.5
2B2810LOOSE POSITIONAL0.495
2B3100MEDIUM THERMAL5.12
2B2810LOOSE THERMAL5.3910
3C803MEDIUM POSITIONAL0.210.5
3C720LOOSE POSITIONAL0.45
3C803MEDIUM THERMAL3.992
3C720LOOSE THERMAL4.4810
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 267 -
Rwork0.341 5299 -
obs--98.44 %

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