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- PDB-3l48: Crystal structure of the C-terminal domain of the PapC usher -

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Basic information

Entry
Database: PDB / ID: 3l48
TitleCrystal structure of the C-terminal domain of the PapC usher
ComponentsOuter membrane usher protein PapC
KeywordsTRANSPORT PROTEIN / Ig fold / greek key / Cell outer membrane / Fimbrium / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell outer membrane
Similarity search - Function
PapC, C-terminal domain / 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 ...PapC, C-terminal domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Outer membrane usher protein PapC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFord, B.A. / Hultgren, S.J.
CitationJournal: J.Bacteriol. / Year: 2010
Title: Structural Homology between the C-Terminal Domain of the PapC Usher and Its Plug.
Authors: Ford, B. / Rego, A.T. / Ragan, T.J. / Pinkner, J. / Dodson, K. / Driscoll, P.C. / Hultgren, S. / Waksman, G.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_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_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 / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane usher protein PapC
B: Outer membrane usher protein PapC
C: Outer membrane usher protein PapC
D: Outer membrane usher protein PapC
E: Outer membrane usher protein PapC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4367
Polymers51,3185
Non-polymers1182
Water4,450247
1
A: Outer membrane usher protein PapC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3232
Polymers10,2641
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane usher protein PapC


Theoretical massNumber of molelcules
Total (without water)10,2641
Polymers10,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Outer membrane usher protein PapC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3232
Polymers10,2641
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Outer membrane usher protein PapC


Theoretical massNumber of molelcules
Total (without water)10,2641
Polymers10,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Outer membrane usher protein PapC


Theoretical massNumber of molelcules
Total (without water)10,2641
Polymers10,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.936, 100.936, 89.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
Outer membrane usher protein PapC


Mass: 10263.684 Da / Num. of mol.: 5 / Fragment: UNP residues 749-836
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / Gene: papC, UTI89_C4893 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q1R2W8
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% Tacsimate pH 8.0, Cryoprotected in 60% Tacsimate and 10% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 19, 2009
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.14 Å / Num. all: 27641 / Num. obs: 27641 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.4 % / Biso Wilson estimate: 24.9 Å2 / Net I/σ(I): 12.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_241)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.14 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 2592 5.03 %random
Rwork0.1995 ---
obs0.2011 27641 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.207 Å2 / ksol: 0.362 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 2 247 3343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033180
X-RAY DIFFRACTIONf_angle_d0.7544352
X-RAY DIFFRACTIONf_dihedral_angle_d15.2191161
X-RAY DIFFRACTIONf_chiral_restr0.05501
X-RAY DIFFRACTIONf_plane_restr0.002584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.33512560.28334865X-RAY DIFFRACTION100
2.1751-2.26220.35962440.34184894X-RAY DIFFRACTION99
2.2622-2.36510.30792410.22594915X-RAY DIFFRACTION100
2.3651-2.48980.25882540.20434917X-RAY DIFFRACTION100
2.4898-2.64580.25332700.21494888X-RAY DIFFRACTION100
2.6458-2.850.24242930.21184847X-RAY DIFFRACTION100
2.85-3.13680.23043070.18824865X-RAY DIFFRACTION100
3.1368-3.59050.20722700.17434890X-RAY DIFFRACTION100
3.5905-4.5230.16622390.14674900X-RAY DIFFRACTION100
4.523-45.15040.17562180.17854950X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.99260.5220.08180.5602-0.33820.3671-0.170.0751-0.0295-0.14970.09570.17490.2144-0.0750.080.2019-0.0172-0.04410.02940.01350.046920.5356-5.2678-32.0752
20.65180.55480.19822.954-0.75030.48210.0167-0.04480.0485-0.6403-0.00460.02010.1265-0.0037-0.17910.2664-0.0466-0.07260.06540.00710.08120.6396-2.6207-34.1961
30.5780.2895-0.06391.4977-0.44751.33290.11230.03630.0880.17920.0690.26990.1834-0.0943-0.17460.1622-0.032-0.05280.05690.02910.1415.8566-3.8157-30.147
42.61421.86462.25611.32071.57331.9699-0.18780.09870.12-0.45540.09220.23560.7151-0.15660.05540.3758-0.1322-0.04890.1656-0.00360.223614.5853-11.4757-30.5189
51.36020.38910.34970.1530.2651.2240.0681-0.04630.20110.23780.0516-0.275-0.1758-0.0388-0.08490.2011-0.027-0.01490.0071-0.0060.123132.947411.2755-20.5364
60.6001-0.75820.1441.10030.04530.62030.05540.04880.06080.16220.0471-0.53780.11120.1405-0.08810.2581-0.0166-0.11720.0854-0.01320.273139.51868.415-17.6608
71.00080.0746-0.31510.92910.23260.66470.0715-0.13730.2540.6395-0.13460.27070.3386-0.10060.04170.4196-0.0199-0.05340.0571-0.0210.117131.02615.3373-12.3402
80.6141.2136-0.17482.6328-0.18690.31290.14290.03050.10910.7761-0.1388-0.0228-0.02170.1819-0.01030.31420.0169-0.03880.10080.00340.132432.167115.03-13.9834
99.3022-1.5508-1.32348.41714.03371.97190.54961.59890.50170.5872-0.3447-0.04690.606-0.5174-0.23090.31830.16340.01630.45540.0550.31227.933618.253-53.5459
102.46150.84790.15711.2742-0.32212.88670.02780.0075-0.1335-0.76690.3704-0.3848-0.20240.1845-0.34180.4148-0.02740.12740.0978-0.02350.209736.76143.6949-39.888
110.6156-0.4119-0.60052.09020.40551.6807-0.15650.00550.1287-0.37680.2949-0.5469-0.45840.3184-0.27180.5142-0.08130.11560.2149-0.01730.303437.59199.8422-40.1532
121.3188-0.175-0.60431.67570.2641.0528-0.00240.08340.2333-0.79790.2726-0.0323-0.3454-0.0281-0.12160.4598-0.09760.01130.10130.01320.114731.87773.4398-43.5915
130.72210.0822-0.61570.11580.07880.8827-0.0206-0.0231-0.1814-0.747-0.0161-0.0337-0.11090.1864-0.08320.4886-0.06120.03610.19950.01430.214632.6973-2.5956-39.6272
140.99470.33950.25760.78930.070.8399-0.0558-0.03080.09831.019-0.14840.2883-0.0119-0.03920.12490.4679-0.0430.08920.0364-0.02460.101921.0426-15.2973-12.0927
152.02331.2965-0.87025.2261-1.69880.751-0.26460.2357-0.46021.22890.0974-0.90970.31210.1350.34130.5965-0.0171-0.0510.00670.04620.060524.8403-19.2193-10.9332
160.4389-0.73230.34712.4534-2.00652.0889-0.0368-0.0522-0.14611.0984-0.06740.874-0.2343-0.07770.08280.4551-0.02590.22780.0544-0.04070.264315.9296-16.0153-12.2634
170.38510.23040.28170.15160.07130.7976-0.0304-0.11520.3653-0.2342-0.12350.7921-0.7784-0.03620.11840.3486-0.01340.07560.0549-0.05410.243116.3984-9.9681-16.0294
180.490.37190.31240.26750.20521.6881-0.0268-0.01620.06280.3192-0.05270.53880.0494-0.09120.07070.17-0.00070.04880.0448-0.05350.249815.274820.2033-18.03
191.4379-0.02970.1091.1528-0.65130.5466-0.3265-0.00210.2311-0.50150.19190.6036-0.3371-0.11020.10.2893-0.0027-0.04880.07-0.02530.302115.957223.7073-22.5138
200.7377-1.13670.12231.8919-0.10750.7418-0.1702-0.0756-0.16430.5498-0.06470.2936-0.0984-0.15580.20020.2688-0.01450.130.0439-0.03990.178815.563721.3751-12.3981
211.4275-0.771-0.17571.83460.38740.56010.1640.0899-0.31940.51210.11140.73020.1946-0.1501-0.23070.323-0.03080.05820.09990.05170.275518.969415.3778-12.8378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 728:755)A728 - 755
2X-RAY DIFFRACTION2(chain A and resid 756:781)A756 - 781
3X-RAY DIFFRACTION3(chain A and resid 782:802)A782 - 802
4X-RAY DIFFRACTION4(chain A and resid 803:808)A803 - 808
5X-RAY DIFFRACTION5(chain B and resid 728:748)B728 - 748
6X-RAY DIFFRACTION6(chain B and resid 749:786)B749 - 786
7X-RAY DIFFRACTION7(chain B and resid 787:801)B787 - 801
8X-RAY DIFFRACTION8(chain B and resid 802:807)B802 - 807
9X-RAY DIFFRACTION9(chain C and resid 722:729)C722 - 729
10X-RAY DIFFRACTION10(chain C and resid 730:755)C730 - 755
11X-RAY DIFFRACTION11(chain C and resid 756:771)C756 - 771
12X-RAY DIFFRACTION12(chain C and resid 772:801)C772 - 801
13X-RAY DIFFRACTION13(chain C and resid 802:807)C802 - 807
14X-RAY DIFFRACTION14(chain D and resid 727:755)D727 - 755
15X-RAY DIFFRACTION15(chain D and resid 756:771)D756 - 771
16X-RAY DIFFRACTION16(chain D and resid 772:801)D772 - 801
17X-RAY DIFFRACTION17(chain D and resid 802:807)D802 - 807
18X-RAY DIFFRACTION18(chain E and resid 729:758)E729 - 758
19X-RAY DIFFRACTION19(chain E and resid 759:771)E759 - 771
20X-RAY DIFFRACTION20(chain E and resid 772:800)E772 - 800
21X-RAY DIFFRACTION21(chain E and resid 801:808)E801 - 808

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