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- PDB-1kiu: FimH adhesin Q133N mutant-FimC chaperone complex with methyl-alph... -

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Basic information

Entry
Database: PDB / ID: 1kiu
TitleFimH adhesin Q133N mutant-FimC chaperone complex with methyl-alpha-D-mannose
Components
  • CHAPERONE PROTEIN FimC
  • FimH PROTEIN
KeywordsCHAPERONE/CELL ADHESION / adhesin-chaperone complex / mannose-bound / CHAPERONE-CELL ADHESION 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 / chaperone-mediated protein folding / 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 / chaperone-mediated protein folding / 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 / FimH, mannose-binding 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / Type 1 fimbrin D-mannose specific adhesin / Chaperone protein FimC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHung, C.S. / Bouckaert, J.
CitationJournal: Mol.Microbiol. / Year: 2002
Title: Structural basis of tropism of Escherichia coli to the bladder during urinary tract infection.
Authors: Hung, C.S. / Bouckaert, J. / Hung, D. / Pinkner, J. / Widberg, C. / DeFusco, A. / Auguste, C.G. / Strouse, R. / Langermann, S. / Waksman, G. / Hultgren, S.J.
History
DepositionDec 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAPERONE PROTEIN FimC
B: FimH PROTEIN
C: CHAPERONE PROTEIN FimC
D: FimH PROTEIN
E: CHAPERONE PROTEIN FimC
F: FimH PROTEIN
G: CHAPERONE PROTEIN FimC
H: FimH PROTEIN
I: CHAPERONE PROTEIN FimC
J: FimH PROTEIN
K: CHAPERONE PROTEIN FimC
L: FimH PROTEIN
M: CHAPERONE PROTEIN FimC
N: FimH PROTEIN
O: CHAPERONE PROTEIN FimC
P: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,88424
Polymers414,33116
Non-polymers1,5538
Water6,792377
1
A: CHAPERONE PROTEIN FimC
B: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,7912
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-14 kcal/mol
Surface area22540 Å2
MethodPISA
2
C: CHAPERONE PROTEIN FimC
D: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,7912
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-14 kcal/mol
Surface area22560 Å2
MethodPISA
3
E: CHAPERONE PROTEIN FimC
F: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,7912
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-14 kcal/mol
Surface area22560 Å2
MethodPISA
4
G: CHAPERONE PROTEIN FimC
H: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,7912
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-14 kcal/mol
Surface area22550 Å2
MethodPISA
5
I: CHAPERONE PROTEIN FimC
J: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,7912
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-15 kcal/mol
Surface area21870 Å2
MethodPISA
6
K: CHAPERONE PROTEIN FimC
L: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,7912
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-15 kcal/mol
Surface area21870 Å2
MethodPISA
7
M: CHAPERONE PROTEIN FimC
N: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,7912
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-15 kcal/mol
Surface area21870 Å2
MethodPISA
8
O: CHAPERONE PROTEIN FimC
P: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,7912
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-15 kcal/mol
Surface area21860 Å2
MethodPISA
9
C: CHAPERONE PROTEIN FimC
D: FimH PROTEIN
hetero molecules

C: CHAPERONE PROTEIN FimC
D: FimH PROTEIN
hetero molecules

I: CHAPERONE PROTEIN FimC
J: FimH PROTEIN
hetero molecules

I: CHAPERONE PROTEIN FimC
J: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,94212
Polymers207,1658
Non-polymers7774
Water1448
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 area21390 Å2
ΔGint-104 kcal/mol
Surface area80610 Å2
MethodPISA
10
A: CHAPERONE PROTEIN FimC
B: FimH PROTEIN
O: CHAPERONE PROTEIN FimC
P: FimH PROTEIN
hetero molecules

G: CHAPERONE PROTEIN FimC
H: FimH PROTEIN
K: CHAPERONE PROTEIN FimC
L: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,94212
Polymers207,1658
Non-polymers7774
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1,-z+11
Buried area21320 Å2
ΔGint-104 kcal/mol
Surface area80640 Å2
MethodPISA
11
E: CHAPERONE PROTEIN FimC
F: FimH PROTEIN
hetero molecules

E: CHAPERONE PROTEIN FimC
F: FimH PROTEIN
hetero molecules

M: CHAPERONE PROTEIN FimC
N: FimH PROTEIN
hetero molecules

M: CHAPERONE PROTEIN FimC
N: FimH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,94212
Polymers207,1658
Non-polymers7774
Water1448
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 area21310 Å2
ΔGint-104 kcal/mol
Surface area80680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.349, 138.334, 213.212
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CHAPERONE PROTEIN FimC / FimC chaperone


Mass: 22724.049 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimC / Plasmid: pMMB60 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P31697
#2: Protein
FimH PROTEIN / FimH adhesin


Mass: 29067.287 Da / Num. of mol.: 8 / Mutation: Q133N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH / Plasmid: pMMB60 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P08191
#3: Sugar
ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.46 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: ammonium sulphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.7 mg/mlprotein1drop
210 mMmethyl-alpha-D-mannopyranoside1reservoir
30.6 Mammonium sulfate1reservoir
4100 mMTris-HCl1reservoirpH8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 20, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→44.46 Å / Num. all: 71767 / Num. obs: 72289 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 63.5 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 10.6
Reflection shellResolution: 3→3.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.51 / % possible all: 87
Reflection
*PLUS
Lowest resolution: 45 Å / % possible obs: 87.1 % / Num. measured all: 197848
Reflection shell
*PLUS
Lowest resolution: 3.11 Å / % possible obs: 65.9 % / Rmerge(I) obs: 0.51

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 7267 10.1 %random
Rwork0.236 ---
all0.236 80000 --
obs0.278 71767 89.1 %-
Solvent computationSolvent model: flat model / Bsol: 56.0908 Å2 / ksol: 0.317169 e/Å3
Displacement parametersBiso mean: 79.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.97 Å2--
2---4.16 Å2-
3---7.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29160 0 104 377 29641
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.92
Refine LS restraints NCSNCS model details: restrained / Weight Biso : 10 / Weight position: 300
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 1209 10.4 %
Rwork0.337 10386 -
obs-71767 87 %
Refinement
*PLUS
Lowest resolution: 45 Å / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0079
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rfree: 0.39 / Rfactor Rwork: 0.36 / Rfactor obs: 0.36

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