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

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Basic information

Entry
Database: PDB / ID: 5iqn
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_SRIRIRGYVR
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 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 1.2Nov 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_struct_conn_angle ...diffrn_radiation_wavelength / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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
Revision 1.4Oct 23, 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
A: Protein FimG
B: Protein FimF
F: Protein FimF
G: Protein FimG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0737
Polymers29,8934
Non-polymers1803
Water8,755486
1
A: Protein FimG
B: Protein FimF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0053
Polymers14,9462
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-15 kcal/mol
Surface area7200 Å2
MethodPISA
2
F: Protein FimF
G: Protein FimG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0674
Polymers14,9462
Non-polymers1212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-15 kcal/mol
Surface area7060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.680, 52.880, 83.140
Angle α, β, γ (deg.)90.00, 98.71, 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 / DsF_SRIRIRGYVR


Mass: 1279.540 Da / Num. of mol.: 2 / Fragment: UNP residues 35-34 / 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.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MOPS-NaOH pH 6.8 (RT), PEG-1500, CoCl2, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.96→50 Å / Num. obs: 133060 / % possible obs: 99.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.064 / Net I/σ(I): 12.9
Reflection shellResolution: 0.96→0.98 Å / Rmerge(I) obs: 1.304 / Rpim(I) all: 1.304

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Processing

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

3bfw


Resolution: 1→25.384 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 13.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.146 5909 5 %
Rwork0.118 --
obs0.1193 118186 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1→25.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 6 486 2590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132459
X-RAY DIFFRACTIONf_angle_d1.4193384
X-RAY DIFFRACTIONf_dihedral_angle_d12.086877
X-RAY DIFFRACTIONf_chiral_restr0.085396
X-RAY DIFFRACTIONf_plane_restr0.009452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.01140.27141910.25983627X-RAY DIFFRACTION98
1.0114-1.02330.24781940.24883686X-RAY DIFFRACTION98
1.0233-1.03570.26031950.22643707X-RAY DIFFRACTION99
1.0357-1.04890.24611940.21873682X-RAY DIFFRACTION99
1.0489-1.06270.23831960.20193731X-RAY DIFFRACTION99
1.0627-1.07720.21571960.18763718X-RAY DIFFRACTION100
1.0772-1.09260.19111960.16923717X-RAY DIFFRACTION100
1.0926-1.10890.19151980.15763773X-RAY DIFFRACTION100
1.1089-1.12620.18491960.14513727X-RAY DIFFRACTION100
1.1262-1.14470.16391950.12833705X-RAY DIFFRACTION100
1.1447-1.16440.13711980.12583755X-RAY DIFFRACTION100
1.1644-1.18560.171950.12953714X-RAY DIFFRACTION100
1.1856-1.20840.16661990.13093768X-RAY DIFFRACTION100
1.2084-1.23310.1511970.12853756X-RAY DIFFRACTION100
1.2331-1.25990.16061960.12333715X-RAY DIFFRACTION100
1.2599-1.28920.15921980.12163767X-RAY DIFFRACTION100
1.2892-1.32140.16221960.11653710X-RAY DIFFRACTION100
1.3214-1.35720.14621990.11463788X-RAY DIFFRACTION100
1.3572-1.39710.1451960.11073719X-RAY DIFFRACTION100
1.3971-1.44220.1451970.10983757X-RAY DIFFRACTION100
1.4422-1.49370.15021970.10883743X-RAY DIFFRACTION100
1.4937-1.55350.13481970.10133745X-RAY DIFFRACTION100
1.5535-1.62420.13251990.09983766X-RAY DIFFRACTION100
1.6242-1.70980.13841990.13784X-RAY DIFFRACTION100
1.7098-1.81690.12121970.09863755X-RAY DIFFRACTION100
1.8169-1.95720.12211990.10183766X-RAY DIFFRACTION100
1.9572-2.1540.11791980.09923766X-RAY DIFFRACTION100
2.154-2.46550.12231980.10623768X-RAY DIFFRACTION100
2.4655-3.10540.14292000.11383803X-RAY DIFFRACTION100
3.1054-25.39220.13492030.10743859X-RAY DIFFRACTION100

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