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- PDB-3bfw: Crystal structure of truncated FimG (FimGt) in complex with the d... -

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Basic information

Entry
Database: PDB / ID: 3bfw
TitleCrystal structure of truncated FimG (FimGt) in complex with the donor strand peptide of FimF (DSF)
Components
  • Protein fimF
  • Protein fimG
KeywordsSTRUCTURAL PROTEIN/STRUCTURAL PROTEIN / Incomplete Ig-like fold / donor strand exchange / Cell projection / Fimbrium / CELL ADHESION / STRUCTURAL PROTEIN-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 / cell adhesion
Similarity search - Function
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
YTTRIUM (III) ION / Protein FimF / Protein FimG
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsEidam, O. / Capitani, G. / Grutter, M.G.
CitationJournal: Structure / Year: 2008
Title: Infinite Kinetic Stability against Dissociation of Supramolecular Protein Complexes through Donor Strand Complementation
Authors: Puorger, C. / Eidam, O. / Capitani, G. / Erilov, D. / Grutter, M.G. / Glockshuber, R.
History
DepositionNov 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein fimG
B: Protein fimF
C: Protein fimG
D: Protein fimF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9005
Polymers30,8114
Non-polymers891
Water6,071337
1
A: Protein fimG
B: Protein fimF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4953
Polymers15,4062
Non-polymers891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-16 kcal/mol
Surface area7040 Å2
MethodPISA
2
C: Protein fimG
D: Protein fimF


Theoretical massNumber of molelcules
Total (without water)15,4062
Polymers15,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-7.9 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.610, 46.740, 48.620
Angle α, β, γ (deg.)92.820, 90.920, 92.510
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein fimG


Mass: 13665.835 Da / Num. of mol.: 2 / Fragment: sequence database residues 36-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: fimG / Plasmid: pTrc99a vector / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P08190
#2: Protein/peptide Protein fimF


Mass: 1739.910 Da / Num. of mol.: 2 / Fragment: sequence database residues 23-37 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P08189
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 1.81 Å3/Da / Density % sol: 32.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM Tris/HCl, pH 8.0, 80 mM NaCl, 27.5% PEG 1500, 20 mM yttrium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91168 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 25, 2005 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91168 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 19304 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 5.3 / % possible all: 96.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementStarting model: PDB ENTRY 3BFQ

3bfq


Resolution: 1.8→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 768 3.8 %RANDOM
Rwork0.204 ---
obs-19304 --
Solvent computationBsol: 67.762 Å2
Displacement parametersBiso mean: 15.214 Å2
Baniso -1Baniso -2Baniso -3
1--3.172 Å20.595 Å20.889 Å2
2--2.062 Å2-0.117 Å2
3---1.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 1 337 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0041.5
X-RAY DIFFRACTIONc_angle_deg0.892
X-RAY DIFFRACTIONc_dihedral_angle_d272
X-RAY DIFFRACTIONc_improper_angle_d0.532.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.235
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3yt3_xplor_par.txt
X-RAY DIFFRACTION4k_xplor_par.txt

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