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- PDB-4dwh: Structure of the major type 1 pilus subunit FIMA bound to the FIM... -

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Basic information

Entry
Database: PDB / ID: 4dwh
TitleStructure of the major type 1 pilus subunit FIMA bound to the FIMC (2.5 A resolution)
Components
  • Chaperone protein fimC
  • Type-1 fimbrial protein, A chain
KeywordsSTRUCTURAL PROTEIN/CHAPERONE / PROTEIN-CHAPERONE COMPLEX / IMMUNOGLOBIN-LIKE FOLD / INVOLVED IN TYPE 1 PILUS ASSEMBLY / STRUCTURAL PROTEIN-CHAPERONE complex
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / identical protein binding
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Type-1 fimbrial protein, A chain / Chaperone protein FimC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsScharer, M.A. / Puorger, C. / Crespo, M. / Glockshuber, R. / Capitani, G.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Quality control of disulfide bond formation in pilus subunits by the chaperone FimC.
Authors: Crespo, M.D. / Puorger, C. / Scharer, M.A. / Eidam, O. / Grutter, M.G. / Capitani, G. / Glockshuber, R.
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Oct 11, 2017Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Sep 13, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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: Chaperone protein fimC
B: Type-1 fimbrial protein, A chain
C: Chaperone protein fimC
D: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,03920
Polymers74,0994
Non-polymers1,94016
Water2,432135
1
A: Chaperone protein fimC
B: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,17712
Polymers37,0502
Non-polymers1,12710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-10 kcal/mol
Surface area15320 Å2
MethodPISA
2
C: Chaperone protein fimC
D: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8638
Polymers37,0502
Non-polymers8136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-8 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.370, 48.810, 113.480
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 1:43 or resseq 47:93 or resseq...
211chain 'C' and (resseq 1:43 or resseq 47:93 or resseq...
112chain 'B' and (resseq 17:89 or resseq 95:114 or resseq 129:159 ) and name ca
212chain 'D' and (resseq 17:89 or resseq 95:114 or resseq 129:159 ) and name ca

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.072917, 0.001934, -0.997336), (0.00792, -0.999968, -0.00136), (-0.997307, -0.0078, -0.07293)52.543301, 54.809601, 56.110401
2given(0.063152, 0.022668, -0.997746), (0.005351, -0.999735, -0.022375), (-0.99799, -0.003926, -0.063257)52.396599, 55.831799, 55.736301
DetailsFimC-FimA heterodimer

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Chaperone protein fimC


Mass: 22754.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b4316, fimC, JW4279 / Plasmid: pFimC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31697
#2: Protein Type-1 fimbrial protein, A chain / Type-1A pilin


Mass: 14295.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b4314, fimA, JW4277, pilA / Plasmid: pFimAt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04128

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Non-polymers , 5 types, 151 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40% (v/v) PEG 400 0.1 M phosphate/citrate pH 4.2 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99986 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 20, 2012
RadiationMonochromator: Fixed exit double, channel DCM Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 2.5→45.26 Å / Num. obs: 23307 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Rmerge(I) obs: 0.203 / Net I/σ(I): 12.05
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.813.60.8563.481100
2.8-30.5185.29199.9
3-3.50.2759.9199.9
3.5-40.15716.811100
4-50.09923.85199.9
5-60.121.71199.8
6-100.08526.271100
10-200.05538.721100
20-250.05837.421100
25-45.260.05237.66183.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
RemDAqdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SQB

3sqb


Resolution: 2.5→45.26 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.41 / Isotropic thermal model: ISOTROPIC / σ(F): 1.35 / Phase error: 31.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2942 792 3.4 %
Rwork0.2327 --
obs0.2348 23296 99.93 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.789 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.9735 Å2-0 Å2-7.2699 Å2
2---5.6784 Å2-0 Å2
3----0.295 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 126 135 5245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045175
X-RAY DIFFRACTIONf_angle_d0.8926986
X-RAY DIFFRACTIONf_dihedral_angle_d12.8531906
X-RAY DIFFRACTIONf_chiral_restr0.061822
X-RAY DIFFRACTIONf_plane_restr0.004902
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A180X-RAY DIFFRACTIONPOSITIONAL0.059
12C180X-RAY DIFFRACTIONPOSITIONAL0.059
21B123X-RAY DIFFRACTIONPOSITIONAL0.051
22D123X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.65680.34081310.27243717X-RAY DIFFRACTION100
2.6568-2.86190.34251320.2733735X-RAY DIFFRACTION100
2.8619-3.14980.33191300.24123702X-RAY DIFFRACTION100
3.1498-3.60540.34251310.23333727X-RAY DIFFRACTION100
3.6054-4.54180.25751330.20923774X-RAY DIFFRACTION100
4.5418-45.26790.2511350.22593849X-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)
10.012-0.03-0.03151.53830.85910.50470.0362-0.0545-0.19290.40710.0094-0.08550.25070.0565-0.00250.1776-0.0204-0.06910.07010.01580.23316.164414.285119.3004
22.0925-2.2114-0.0634.4063-0.08161.0767-0.2233-0.2317-0.00620.33360.21310.00040.0642-0.1022-0.0050.08330.0118-0.03820.07180.02490.149110.262825.332317.821
32.1018-0.0352-0.48051.9014-0.01531.46990.10190.48220.2601-0.4416-0.04680.2485-0.0872-0.2053-0.00910.2650.0237-0.08750.16790.01590.234618.993812.1871-7.5157
44.50840.14710.09494.9103-0.4674.60850.32930.57880.0537-0.1191-0.0483-0.0488-0.41850.3756-0.25120.09450.04040.03610.1615-0.00090.207626.693416.9016-4.5554
52.58060.4790.47271.13830.28351.65150.0030.07520.3017-0.07360.02450.1281-0.0977-0.27660.0150.1721-0.0945-0.08690.14730.1110.19363.903136.446612.5185
60.0082-0.00020.01110.0270.01840.0269-0.13550.41950.08810.13670.0485-0.3808-0.0823-0.23450.08570.3332-0.0349-0.26710.4275-0.00020.46217.215132.27184.223
72.3081-0.15350.12921.5071-0.51451.12080.0994-0.14520.1267-0.1340.00250.1842-0.0351-0.3740.04990.10620.0167-0.09340.182-0.06430.1571.832135.933812.1653
80.19680.20410.01350.4130.0136-0.0062-0.0249-0.00560.2277-0.18880.02510.2212-0.0316-0.04050.00410.09270.1332-0.34270.00380.02540.293233.489240.080439.4047
91.12610.12520.03432.9037-0.87661.3263-0.03710.07490.1297-0.25960.0806-0.0157-0.0409-0.06160.00280.12840.0003-0.14630.00750.02220.149840.593536.895839.587
103.6211-0.3286-1.6394.07450.49612.2095-0.1942-0.17830.27410.556-0.1405-0.44260.14180.38990.23280.2379-0.0588-0.10730.17080.00390.221962.328641.164238.9078
110.1795-0.7295-0.06842.99440.29093.2587-0.3094-0.0370.27590.3089-0.062-0.3224-0.0770.52240.23920.33030.0006-0.11850.20040.03840.37361.178639.507736.0419
120.9234-0.06050.31620.59-0.24541.6479-0.081-0.4005-0.14310.1410.0439-0.09260.13610.0827-0.07370.20780.1402-0.21060.2628-0.01610.227240.857918.829351.3821
137.34095.60867.3495.33045.80028.71420.1182-0.2209-0.45971.6289-0.0138-0.6561.85611.4011-0.10280.61640.0658-0.12640.37270.02840.378248.869624.686543.4382
142.3472-0.41660.74261.3597-0.15921.2113-0.1361-0.46670.08420.13380.02580.0947-0.188-0.1701-0.44770.17960.0139-0.20180.2539-0.03650.256240.170818.898353.6188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:87)
2X-RAY DIFFRACTION2(chain A and resid 88:116)
3X-RAY DIFFRACTION3(chain A and resid 117:184)
4X-RAY DIFFRACTION4(chain A and resid 185:204)
5X-RAY DIFFRACTION5(chain B and resid 17:104)
6X-RAY DIFFRACTION6(chain B and resid 105:129)
7X-RAY DIFFRACTION7(chain B and resid 130:159)
8X-RAY DIFFRACTION8(chain C and resid 1:92)
9X-RAY DIFFRACTION9(chain C and resid 93:128)
10X-RAY DIFFRACTION10(chain C and resid 129:165)
11X-RAY DIFFRACTION11(chain C and resid 166:205)
12X-RAY DIFFRACTION12(chain D and resid 17:114)
13X-RAY DIFFRACTION13(chain D and resid 115:129)
14X-RAY DIFFRACTION14(chain D and resid 130:159)

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