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- PDB-5iqm: Crystal structure of the E. coli type 1 pilus subunit FimG (engin... -

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Basic information

Entry
Database: PDB / ID: 5iqm
TitleCrystal structure of the E. coli type 1 pilus subunit FimG (engineered variant with substitution Q134E; N-terminal FimG residues 1-12 truncated) in complex with the donor strand peptide DsF_T4R-T6R-D13N
Components
  • Protein FimF
  • Protein FimG
KeywordsCELL ADHESION / Complex / Protein / FimGt
Function / homology
Function and homology information


pilus assembly / 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
: / Protein FimF / Protein FimG
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGiese, C. / Eras, J. / Kern, A. / Scharer, M.A. / Capitani, G. / Glockshuber, R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Accelerating the Association of the Most Stable Protein-Ligand Complex by More than Two Orders of Magnitude.
Authors: Giese, C. / Eras, J. / Kern, A. / Scharer, M.A. / Capitani, G. / Glockshuber, R.
History
DepositionMar 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Protein FimG
A: Protein FimG
F: Protein FimF
B: Protein FimF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0718
Polymers30,8364
Non-polymers2364
Water7,548419
1
G: Protein FimG
F: Protein FimF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5955
Polymers15,4182
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-21 kcal/mol
Surface area7160 Å2
MethodPISA
2
A: Protein FimG
B: Protein FimF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4773
Polymers15,4182
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-21 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.190, 62.120, 50.640
Angle α, β, γ (deg.)90.00, 108.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein FimG


Mass: 13666.820 Da / Num. of mol.: 2 / Fragment: UNP residues 36-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimG, b4319, JW4282 / Production host: Escherichia coli (E. coli) / References: UniProt: P08190
#2: Protein/peptide Protein FimF


Mass: 1750.963 Da / Num. of mol.: 2 / Fragment: UNP residues 23-37 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) / References: UniProt: P08189
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MOPS-NaOH pH 7.0 (RT), PEG-1500, NaCl, CoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 88780 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellLowest resolution: 1.54 Å / Redundancy: 1.5 % / Rmerge(I) obs: 1.182

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bfq

3bfq


Resolution: 1.5→47.889 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.4
RfactorNum. reflection% reflection
Rfree0.185 1770 1.99 %
Rwork0.1509 --
obs0.1516 88777 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→47.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 4 419 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092317
X-RAY DIFFRACTIONf_angle_d1.183182
X-RAY DIFFRACTIONf_dihedral_angle_d11.939819
X-RAY DIFFRACTIONf_chiral_restr0.047377
X-RAY DIFFRACTIONf_plane_restr0.005429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54060.25011410.25036776X-RAY DIFFRACTION100
1.5406-1.58590.25131340.23316595X-RAY DIFFRACTION100
1.5859-1.63710.2611370.22486743X-RAY DIFFRACTION100
1.6371-1.69560.23471360.20696669X-RAY DIFFRACTION100
1.6956-1.76350.21151350.19436655X-RAY DIFFRACTION100
1.7635-1.84380.17551370.16716674X-RAY DIFFRACTION100
1.8438-1.9410.1931350.15076710X-RAY DIFFRACTION100
1.941-2.06260.2031380.14866678X-RAY DIFFRACTION100
2.0626-2.22180.17721370.13846722X-RAY DIFFRACTION100
2.2218-2.44540.15891340.13386675X-RAY DIFFRACTION100
2.4454-2.79920.19211370.13856718X-RAY DIFFRACTION100
2.7992-3.52660.21371370.13846669X-RAY DIFFRACTION100
3.5266-47.91290.13361320.1286723X-RAY DIFFRACTION100

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