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- PDB-6r74: N-terminally reversed variant of FimA E. coli -

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Basic information

Entry
Database: PDB / ID: 6r74
TitleN-terminally reversed variant of FimA E. coli
ComponentsType-1 fimbrial protein, A chain
KeywordsSTRUCTURAL PROTEIN / FimA / pilus / monomer / subunit / pili / synthetic / construct / main structural subunit / high resolution / N terminus / reversed
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / cell adhesion involved in single-species biofilm formation / Adhesion domain superfamily / pilus / cell adhesion / identical protein binding / Type-1 fimbrial protein, A chain
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsZyla, D. / Echeverria, B. / Glockshuber, R.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_176403/1 Switzerland
Swiss National Science Foundation31003A_156304 Switzerland
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Donor strand sequence, rather than donor strand orientation, determines the stability and non-equilibrium folding of the type 1 pilus subunit FimA.
Authors: Zyla, D. / Echeverria, B. / Glockshuber, R.
History
DepositionMar 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3166
Polymers15,8351
Non-polymers4805
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Superdex 75 10 30 gave a single peak corresponding to the protein of a mass of ~15-20 kDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.550, 86.550, 164.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-201-

SO4

31A-360-

HOH

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Components

#1: Protein Type-1 fimbrial protein, A chain / Type-1A pilin


Mass: 15835.243 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimA, pilA, b4314, JW4277 / Production host: Escherichia coli (E. coli) / References: UniProt: P04128
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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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: 3.31 Å3/Da / Density % sol: 62.8 %
Description: heterogeneous plates, spread mostly in 2 dimentions
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.1 / Details: 45% NH4SO2 and 0.1M Sodium Malonate buffer pH 3.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 16, 2018
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→43.275 Å / Num. obs: 21875 / % possible obs: 99.8 % / Redundancy: 9.609 % / Biso Wilson estimate: 37.606 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.176 / Χ2: 1.046 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.81-1.865.0031.890.8616000.5912.11499.8
1.86-1.914.9271.3381.1915610.5651.49999.9
1.91-1.964.7190.9821.5914900.7921.10499.1
1.96-2.025.431.1482.1514720.8071.24899.5
2.02-2.0911.731.5393.0614170.9041.6199.9
2.09-2.1611.9361.1254.0113930.9651.176100
2.16-2.2511.9181.034.4413340.941.076100
2.25-2.3411.8810.7915.5212950.9520.827100
2.34-2.4411.7510.6266.3912360.9740.655100
2.44-2.5611.5520.4868.6411960.9780.509100
2.56-2.711.6410.37810.4711170.9850.395100
2.7-2.8611.4390.27813.0110880.990.291100
2.86-3.0611.1930.19915.349940.9930.209100
3.06-3.310.7610.14219.269450.9950.149100
3.3-3.629.6730.10922.438710.9930.11699.9
3.62-4.0510.0740.08426.657960.9970.08999.6
4.05-4.6711.6880.0731.987030.9980.074100
4.67-5.7211.5910.06533.876140.9990.068100
5.72-8.0911.2570.06334.064710.9950.067100
8.09-43.2759.830.06133.582820.9970.06598.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NKT

5nkt


Resolution: 1.81→43.275 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 1091 4.99 %Random selection
Rwork0.1888 ---
obs0.1903 21851 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.38 Å2 / Biso mean: 48.9839 Å2 / Biso min: 22.19 Å2
Refinement stepCycle: final / Resolution: 1.81→43.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 30 87 1220
Biso mean--95.27 44.88 -
Num. residues----157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.89240.36081350.335325532688100
1.8924-1.99210.28221320.26342530266299
1.9921-2.1170.23391360.213725892725100
2.117-2.28040.20831340.180525522686100
2.2804-2.50990.20921360.17426102746100
2.5099-2.8730.18631370.167325912728100
2.873-3.61940.1621370.167626132750100
3.6194-43.28740.24761440.188127222866100
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)
10.9358-0.239-0.04451.3071-0.32960.1475-0.19240.67890.0448-0.8897-0.2382-0.1009-0.03530.29270.00020.7041-0.00470.06060.6240.04770.4384-4.422212.388-35.8696
20.62630.00410.10670.4899-0.48530.49990.1618-0.27260.07650.3102-0.12370.2787-0.51430.0167-0.00090.4273-0.01020.0550.30380.00590.3557-1.590812.9611-14.1502
30.8407-0.11170.23440.01860.03671.36380.10880.7765-0.3117-1.33850.1178-0.00650.31630.874-0.01721.0731-0.0112-0.1110.5207-0.03440.4841-6.45437.6396-40.0151
41.4490.249-0.93940.0428-0.16150.6091-0.32820.262-0.2302-0.5643-0.01380.47710.5053-0.847-0.28190.8704-0.122-0.2890.57490.00490.5046-18.56729.3289-42.3379
50.4355-0.23330.07391.9953-0.6020.85010.12590.04770.0307-0.36970.19940.30310.2684-0.1957-0.00010.3071-0.0087-0.01080.30510.05620.3683-10.453612.546-20.841
61.5684-1.25680.40052.94331.31721.69730.28360.2468-0.0386-0.75970.08450.5030.4735-0.4012-0.00040.4984-0.018-0.10280.33920.08550.3852-12.886615.3469-34.259
70.4444-0.0027-0.33240.32-0.14250.31140.10960.1032-0.0457-0.13840.17420.45490.0921-0.0803-0.00190.310.01020.02410.27590.07940.4242-12.55658.9403-14.5439
81.5939-0.61660.14391.2320.54880.38060.29710.4935-0.0424-0.9139-0.07090.33980.27790.28420.0050.6461-0.0194-0.12360.39660.07150.3817-11.674210.7419-35.775
90.5947-0.24770.62471.7328-0.0431.22710.16620.24460.11460.2210.18120.2646-0.9998-0.5596-0.00170.37210.0390.00750.34650.04620.4354-8.173516.0638-19.5582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A1 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 28 )A15 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 41 )A29 - 41
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 51 )A42 - 51
5X-RAY DIFFRACTION5chain 'A' and (resid 52 through 84 )A52 - 84
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 114 )A85 - 114
7X-RAY DIFFRACTION7chain 'A' and (resid 115 through 128 )A115 - 128
8X-RAY DIFFRACTION8chain 'A' and (resid 129 through 149 )A129 - 149
9X-RAY DIFFRACTION9chain 'A' and (resid 150 through 159 )A150 - 159

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