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- PDB-6r7e: N-terminally reversed variant of FimA E. coli with alanine insert... -

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Basic information

Entry
Database: PDB / ID: 6r7e
TitleN-terminally reversed variant of FimA E. coli with alanine insertion at position 20
ComponentsFimA
KeywordsSTRUCTURAL PROTEIN / FimA / pilus / monomer / subunit / pili / synthetic / construct / main structural subunit / high resolution / N terminus / reversed
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / cell adhesion / identical protein binding
Similarity search - Function
Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
Type-1 fimbrial protein, A chain / FimA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 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
Revision 1.4Nov 20, 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: FimA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0983
Polymers15,9061
Non-polymers1922
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Single peak corresponding to the protein of a size of 15-20 kDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.100, 87.100, 163.200
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-202-

SO4

21A-341-

HOH

31A-354-

HOH

41A-427-

HOH

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Components

#1: Protein FimA / Fimbrial protein / Type-1 fimbrial protein subunit A / Type-1 fimbrial protein / A chain


Mass: 15906.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: fimA, fimA_3, fimA_4, AKG99_10950, AM464_16225, AUQ13_11250, B1K96_24765, B9M99_24745, B9T59_08995, C4J69_04805, C5P44_07805, C6B13_05790, CIJ94_16820, CR538_22075, DNQ45_01525, DS732_03935, ...Gene: fimA, fimA_3, fimA_4, AKG99_10950, AM464_16225, AUQ13_11250, B1K96_24765, B9M99_24745, B9T59_08995, C4J69_04805, C5P44_07805, C6B13_05790, CIJ94_16820, CR538_22075, DNQ45_01525, DS732_03935, DTM27_25935, ECONIH1_25830, HMPREF3040_05526, MS6198_50780, NCTC9010_04482, NCTC9036_04290, NCTC9117_05374, SAMEA3472056_01238
Production host: Escherichia coli (E. coli) / References: UniProt: Q547G4, UniProt: P04128*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.74 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.1 / Details: 45% NH4SO2 and 0.1 M 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: Apr 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: 1.7→43.55 Å / Num. obs: 26259 / % possible obs: 99.3 % / Redundancy: 10.094 % / Biso Wilson estimate: 32.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.145 / Χ2: 1.075 / Net I/σ(I): 10.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.7510.2687.9690.2118920.1228.37798.2
1.75-1.810.545.6760.3318690.1095.9698.7
1.8-1.8510.4954.5080.4818150.1764.73598.9
1.85-1.9110.3693.0080.7717620.2773.16198.8
1.91-1.9710.2352.0581.1517080.4222.16499
1.97-2.049.971.331.8616590.6681.40299.1
2.04-2.119.30.9612.4616020.7761.01799.3
2.11-2.210.320.6973.6915480.8970.73399.3
2.2-2.310.1430.5754.3914760.9160.60699.4
2.3-2.419.5540.485.0514340.9350.50799.4
2.41-2.5410.3470.3257.7913540.9730.34299.6
2.54-2.6910.5380.24210.4112860.9870.25499.6
2.69-2.8810.4110.15915.2212210.9930.16799.8
2.88-3.1110.2230.12419.111400.9960.1399.5
3.11-3.419.8880.07628.1610410.9980.0899.9
3.41-3.819.0070.05235.899600.9990.055100
3.81-4.49.9780.04244.138530.9990.04499.9
4.4-5.399.2940.03747.987250.9990.039100
5.39-7.6210.1970.03849.395740.9990.041100
7.62-43.559.0260.02954.853400.9990.03199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5nkt


Resolution: 1.79→43.55 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.98
RfactorNum. reflection% reflection
Rfree0.2007 1136 5 %
Rwork0.1752 --
obs0.1765 22729 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.24 Å2 / Biso mean: 55.233 Å2 / Biso min: 23.45 Å2
Refinement stepCycle: final / Resolution: 1.79→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 10 161 1276
Biso mean--50.62 52.56 -
Num. residues----159
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 (%)
1.7901-1.87150.29851390.31052641278099
1.8715-1.97020.28481400.247426702810100
1.9702-2.09370.27391400.207926562796100
2.0937-2.25530.22591420.172426922834100
2.2553-2.48220.17871410.167626882829100
2.4822-2.84140.18591420.161726872829100
2.8414-3.57960.19321440.163827342878100
3.5796-43.56290.18661480.167628252973100
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)
10.2123-0.2344-0.00770.534-0.14740.0818-0.04850.34640.0386-0.52720.03810.02260.15140.17850.01960.6461-0.04550.03370.4910.05010.3256-4.622412.9057-34.7547
20.21950.00380.1550.1688-0.19460.24070.1799-0.15720.3735-0.07560.11620.3007-0.61-0.07600.41340.03320.04670.34580.01020.4417-2.741813.7649-13.9514
32.3743-0.0630.90770.09710.46183.5570.01210.33530.3419-1.3408-0.20860.04780.57610.0511-0.18891.04-0.0907-0.10170.37370.00130.4373-7.37298.4296-39.9193
40.8388-0.3704-0.66830.15580.28950.5335-0.03220.57130.0354-0.4531-0.09710.33740.1073-0.4883-0.0161.1981-0.2576-0.56060.5498-0.0330.5093-19.2899.4715-41.8577
50.43890.55470.37431.02940.18430.6776-0.01570.00810.0293-0.29970.25510.25470.1887-0.11830.04070.32890.014-0.00740.31240.07460.3474-10.633312.6061-20.7897
60.4486-0.53880.1790.8142-0.11690.1274-0.05390.2905-0.012-1.05420.41450.68290.4594-0.4255-0.04370.6907-0.1161-0.0860.41380.13620.4243-12.583915.7268-34.9129
71.115-0.2853-0.03351.29620.55930.30150.02010.1593-0.0577-0.6430.30.44740.0679-0.2060.26180.5044-0.0863-0.1020.30830.06850.3767-12.257310.1668-27.333
80.09380.16250.1060.2410.01270.1241-0.03310.14470.1418-0.23260.34520.3281-0.2267-0.22350.00210.43530.0340.0390.32730.06420.3493-8.495516.1578-19.4472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )A1 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 28 )A14 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 42 )A29 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 51 )A43 - 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 149 )A115 - 149
8X-RAY DIFFRACTION8chain 'A' and (resid 150 through 159 )A150 - 159

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