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- PDB-1klf: FIMH ADHESIN-FIMC CHAPERONE COMPLEX WITH D-MANNOSE -

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Basic information

Entry
Database: PDB / ID: 1klf
TitleFIMH ADHESIN-FIMC CHAPERONE COMPLEX WITH D-MANNOSE
Components
  • CHAPERONE PROTEIN FIMC
  • FIMH PROTEIN
KeywordsCHAPERONE/ADHESIN COMPLEX / ADHESIN-CHAPERONE COMPLEX / MANNOSE-BOUND / CHAPERONE-ADHESIN COMPLEX COMPLEX
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 / 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 / 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
alpha-D-mannopyranose / 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: 2.79 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 11, 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.name / _chem_comp.type ..._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 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH ...BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 16CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOMOLECULES ARE 1, 2, 3, 4, 5, 6, 7 AND 8 RESPECTIVELY, EACH CONSISTING OF A COMPLEX OF CHAPERONE FIMC WITH ADHESIN FIMH. THERE IS NO BIOLOGICALLY SIGNIFICANT HIGHER OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Polymers414,44316
Non-polymers1,4418
Water8,917495
1
A: CHAPERONE PROTEIN FIMC
B: FIMH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,8052
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-14 kcal/mol
Surface area21740 Å2
MethodPISA
2
C: CHAPERONE PROTEIN FIMC
D: FIMH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,8052
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-14 kcal/mol
Surface area21730 Å2
MethodPISA
3
E: CHAPERONE PROTEIN FIMC
F: FIMH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,8052
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-14 kcal/mol
Surface area21730 Å2
MethodPISA
4
G: CHAPERONE PROTEIN FIMC
H: FIMH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,8052
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-14 kcal/mol
Surface area21720 Å2
MethodPISA
5
I: CHAPERONE PROTEIN FIMC
J: FIMH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,8052
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-12 kcal/mol
Surface area22250 Å2
MethodPISA
6
K: CHAPERONE PROTEIN FIMC
L: FIMH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,8052
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-12 kcal/mol
Surface area22240 Å2
MethodPISA
7
M: CHAPERONE PROTEIN FIMC
N: FIMH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,8052
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-12 kcal/mol
Surface area22250 Å2
MethodPISA
8
O: CHAPERONE PROTEIN FIMC
P: FIMH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,8052
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-13 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.077, 138.130, 215.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121
Details1 chaperone - 1 adhesin - 1 mannose is one biological assembly

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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: PMMB66 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P31697
#2: Protein
FIMH PROTEIN / FIMH ADHESIN


Mass: 29081.314 Da / Num. of mol.: 8
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-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.48 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: ammonium suplhate, pH 8.20, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.7 mg/mlprotein1drop
220 mMMES1droppH6.5
37 mMalpha-D-mannose1drop
41.0 Mammonium sulfate1reservoir
5100 mMTris-HCl1reservoirpH8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 / Wavelength: 0.9793 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 18, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.79→43.68 Å / Num. all: 100438 / Num. obs: 99135 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 66.3 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 13
Reflection shellResolution: 2.79→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.478 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. measured all: 370427
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 99.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QUN

1qun


Resolution: 2.79→43.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1364705.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.28 9936 9.9 %RANDOM
Rwork0.239 ---
all0.239 100438 --
obs0.239 99135 98.9 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 96.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2--
2---2.9 Å2-
3---4.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.79→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29184 0 96 495 29775
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED / Weight Biso : 8 / Weight position: 250
LS refinement shellResolution: 2.79→2.96 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 1564 10.1 %
Rwork0.355 13965 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.42 / Rfactor Rwork: 0.35 / Rfactor obs: 0.35

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