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- PDB-3ohn: Crystal structure of the FimD translocation domain -

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Basic information

Entry
Database: PDB / ID: 3ohn
TitleCrystal structure of the FimD translocation domain
ComponentsOuter membrane usher protein FimD
KeywordsMEMBRANE PROTEIN / beta-barrel / protein translocation / outer membrane
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell outer membrane / membrane => GO:0016020
Similarity search - Function
Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain
Similarity search - Domain/homology
Outer membrane usher protein FimD / Outer membrane usher protein FimD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.011 Å
AuthorsWang, T. / Li, H.
CitationJournal: Nature / Year: 2011
Title: Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate.
Authors: Phan, G. / Remaut, H. / Wang, T. / Allen, W.J. / Pirker, K.F. / Lebedev, A. / Henderson, N.S. / Geibel, S. / Volkan, E. / Yan, J. / Kunze, M.B. / Pinkner, J.S. / Ford, B. / Kay, C.W. / Li, H. ...Authors: Phan, G. / Remaut, H. / Wang, T. / Allen, W.J. / Pirker, K.F. / Lebedev, A. / Henderson, N.S. / Geibel, S. / Volkan, E. / Yan, J. / Kunze, M.B. / Pinkner, J.S. / Ford, B. / Kay, C.W. / Li, H. / Hultgren, S.J. / Thanassi, D.G. / Waksman, G.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _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: Outer membrane usher protein FimD
B: Outer membrane usher protein FimD


Theoretical massNumber of molelcules
Total (without water)123,0752
Polymers123,0752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Outer membrane usher protein FimD

B: Outer membrane usher protein FimD


Theoretical massNumber of molelcules
Total (without water)123,0752
Polymers123,0752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
Buried area1630 Å2
ΔGint-17 kcal/mol
Surface area45750 Å2
MethodPISA
3
A: Outer membrane usher protein FimD

B: Outer membrane usher protein FimD


Theoretical massNumber of molelcules
Total (without water)123,0752
Polymers123,0752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1890 Å2
ΔGint-15 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.022, 87.132, 95.883
Angle α, β, γ (deg.)63.92, 88.43, 76.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Outer membrane usher protein FimD


Mass: 61537.316 Da / Num. of mol.: 2 / Fragment: TRANSLOCATION DOMAIN (unp residues 169-708)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimD / Plasmid: pNH297 / Production host: Escherichia coli (E. coli) / Strain (production host): B tuner / References: UniProt: C8U0R5, UniProt: P30130*PLUS

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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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM Trisodium citrate,pH4.8~6.5, 7% (w/v) PEG4000, 100mM sodium chloride, 50mM Magnesium, 20mM spermine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 27375 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.115
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.5 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERPHENIXphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2vqi

2vqi


Resolution: 3.011→28.89 Å / SU ML: 0.44 / σ(F): 1.97 / Phase error: 33.22 / Stereochemistry target values: ML
Details: AUTHORS HAVE APPROVED THIS ENTRY WITH REPORTED R VALUE AS 0.23 WHILE CALCULATED R VALUE IS 0.31. THE DEPOSITED COORDINATES WERE FURTHER MODIFIED IN COOT AFTER FINAL ROUND OF PHENIX REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.3053 1368 5 %random
Rwork0.2295 ---
obs0.2334 27375 98.04 %-
all-27410 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.835 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 61.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.2886 Å24.2899 Å2-5.1891 Å2
2--18.7583 Å2-5.878 Å2
3----10.4697 Å2
Refinement stepCycle: LAST / Resolution: 3.011→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7246 0 0 0 7246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097426
X-RAY DIFFRACTIONf_angle_d1.38710068
X-RAY DIFFRACTIONf_dihedral_angle_d18.112603
X-RAY DIFFRACTIONf_chiral_restr0.091061
X-RAY DIFFRACTIONf_plane_restr0.0051323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0113-3.11880.37841280.26992526X-RAY DIFFRACTION94
3.1188-3.24350.35841250.24272607X-RAY DIFFRACTION99
3.2435-3.39090.30011230.22692601X-RAY DIFFRACTION98
3.3909-3.56930.27851300.20832645X-RAY DIFFRACTION99
3.5693-3.79250.28031560.20212612X-RAY DIFFRACTION99
3.7925-4.08460.29411190.20792631X-RAY DIFFRACTION99
4.0846-4.49430.24641460.18972609X-RAY DIFFRACTION99
4.4943-5.14140.25891250.18782627X-RAY DIFFRACTION99
5.1414-6.46570.33071580.25752599X-RAY DIFFRACTION98
6.4657-28.89160.331580.26712550X-RAY DIFFRACTION97

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