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- PDB-3fip: Crystal structure of Usher PapC translocation pore -

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Basic information

Entry
Database: PDB / ID: 3fip
TitleCrystal structure of Usher PapC translocation pore
ComponentsOuter membrane usher protein papC
KeywordsTRANSPORT PROTEIN / beta barrel / protein translocase / Cell membrane / Cell outer membrane / Fimbrium / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell outer membrane / identical protein binding
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 PapC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.154 Å
AuthorsHuang, Y. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Insights into pilus assembly and secretion from the structure and functional characterization of usher PapC.
Authors: Huang, Y. / Smith, B.S. / Chen, L.X. / Baxter, R.H. / Deisenhofer, J.
History
DepositionDec 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 28, 2011Group: Derived calculations
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 papC
B: Outer membrane usher protein papC


Theoretical massNumber of molelcules
Total (without water)109,7222
Polymers109,7222
Non-polymers00
Water00
1
A: Outer membrane usher protein papC


Theoretical massNumber of molelcules
Total (without water)54,8611
Polymers54,8611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer membrane usher protein papC


Theoretical massNumber of molelcules
Total (without water)54,8611
Polymers54,8611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.036, 120.036, 354.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Outer membrane usher protein papC


Mass: 54861.133 Da / Num. of mol.: 2 / Fragment: PapC translocation core
Source method: isolated from a genetically manipulated source
Details: with C-terminal His tag / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Escherichia coli Enterobacteriaceae, papC / Plasmid: pBAD-PAPC / Production host: Escherichia coli (E. coli) / Strain (production host): sf120 strain / References: UniProt: P07110

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.9
Details: 3.3M NaCl, 0.06%LDAO, 4% 2,5 hexanidiol, 20mM Tris, pH 4.9, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 41032 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 90.2 Å2 / Rsym value: 0.084 / Net I/σ(I): 34.8
Reflection shellHighest resolution: 3.15 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.546

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Processing

Software
NameVersionClassification
HKL-3000data collection
SnBphasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.154→49.679 Å / SU ML: 0.86 / σ(F): 1.89 / Phase error: 38.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.359 2110 5.15 %
Rwork0.2853 --
obs0.289 41007 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.584 Å2 / ksol: 0.294 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.9538 Å20 Å20 Å2
2--12.9538 Å20 Å2
3----25.9076 Å2
Refinement stepCycle: LAST / Resolution: 3.154→49.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6295 0 0 0 6295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016396
X-RAY DIFFRACTIONf_angle_d1.378639
X-RAY DIFFRACTIONf_dihedral_angle_d22.0652166
X-RAY DIFFRACTIONf_chiral_restr0.088944
X-RAY DIFFRACTIONf_plane_restr0.0051112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1544-3.22780.38951290.32771968X-RAY DIFFRACTION75
3.2278-3.30850.39091540.33462357X-RAY DIFFRACTION88
3.3085-3.39790.46981360.31122552X-RAY DIFFRACTION95
3.3979-3.49790.39551330.30772636X-RAY DIFFRACTION98
3.4979-3.61080.39031120.29622744X-RAY DIFFRACTION99
3.6108-3.73980.41821560.32382658X-RAY DIFFRACTION100
3.7398-3.88940.4391330.31822674X-RAY DIFFRACTION100
3.8894-4.06640.36221660.27772669X-RAY DIFFRACTION100
4.0664-4.28070.30311520.24892670X-RAY DIFFRACTION100
4.2807-4.54870.33181590.21792697X-RAY DIFFRACTION100
4.5487-4.89960.26861430.20612672X-RAY DIFFRACTION99
4.8996-5.39210.34851430.24232665X-RAY DIFFRACTION100
5.3921-6.17110.37871420.28972678X-RAY DIFFRACTION100
6.1711-7.77020.34381160.29592715X-RAY DIFFRACTION99
7.7702-49.68550.3541360.30442542X-RAY DIFFRACTION93

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