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- PDB-6erj: Self-complemented FimA subunit from Salmonella enterica -

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Basic information

Entry
Database: PDB / ID: 6erj
TitleSelf-complemented FimA subunit from Salmonella enterica
Components(Type-1 fimbrial protein, a chain) x 2
KeywordsSTRUCTURAL PROTEIN / FimA / subunit / pilus / pili / tyle-1 pilus / type-1 pili / salmonella / enterica / immunoglobulin-like / fold / self-complemented
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / ACETIC ACID / Type 1 fimbrial protein subunit FimA
Function and homology information
Biological speciesSalmonella paratyphi A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsZyla, D.S. / Prota, A. / Capitani, G. / Glockshuber, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation156304 Switzerland
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Alternative folding to a monomer or homopolymer is a common feature of the type 1 pilus subunit FimA from enteroinvasive bacteria.
Authors: Zyla, D.S. / Prota, A.E. / Capitani, G. / Glockshuber, R.
History
DepositionOct 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
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 / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jul 17, 2019Group: Data collection / 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
Revision 1.3Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 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
B: Type-1 fimbrial protein, a chain
A: Type-1 fimbrial protein, a chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5625
Polymers33,3822
Non-polymers1803
Water3,981221
1
B: Type-1 fimbrial protein, a chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8473
Polymers16,7261
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Type-1 fimbrial protein, a chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7152
Polymers16,6551
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.970, 104.430, 182.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

21A-398-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 15 or (resid 17...
21(chain B and (resid 5 through 15 or (resid 17...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHE(chain A and (resid 5 through 15 or (resid 17...AB5 - 155 - 15
12GLYGLYALAALA(chain A and (resid 5 through 15 or (resid 17...AB17 - 2317 - 23
13ASPASPGLUGLU(chain A and (resid 5 through 15 or (resid 17...AB2 - 1632 - 163
14ASPASPGLUGLU(chain A and (resid 5 through 15 or (resid 17...AB2 - 1632 - 163
15ASPASPGLUGLU(chain A and (resid 5 through 15 or (resid 17...AB2 - 1632 - 163
16ASPASPGLUGLU(chain A and (resid 5 through 15 or (resid 17...AB2 - 1632 - 163
21PROPROPHEPHE(chain B and (resid 5 through 15 or (resid 17...BA5 - 156 - 16
22GLYGLYALAALA(chain B and (resid 5 through 15 or (resid 17...BA17 - 2318 - 24
23THRTHRGLUGLU(chain B and (resid 5 through 15 or (resid 17...BA4 - 1635 - 164
24THRTHRGLUGLU(chain B and (resid 5 through 15 or (resid 17...BA4 - 1635 - 164
25THRTHRGLUGLU(chain B and (resid 5 through 15 or (resid 17...BA4 - 1635 - 164
26THRTHRGLUGLU(chain B and (resid 5 through 15 or (resid 17...BA4 - 1635 - 164

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Components

#1: Protein Type-1 fimbrial protein, a chain


Mass: 16726.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella paratyphi A (strain ATCC 9150 / SARB42) (bacteria)
Strain: ATCC 9150 / SARB42 / Gene: fimA, SPA2182 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2WR29
#2: Protein Type-1 fimbrial protein, a chain


Mass: 16655.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella paratyphi A (strain ATCC 9150 / SARB42) (bacteria)
Strain: ATCC 9150 / SARB42 / Gene: fimA, SPA2182 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2WR29
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Description: very irregular, growing mostly to in 2 dimentions
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.255 M Ammonium Sulphate 29.5% PEG 4k 15% glycerol 18 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2016
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→45.718 Å / Num. obs: 38168 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 15.163 % / Biso Wilson estimate: 27.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.122 / Χ2: 1.105 / Net I/σ(I): 12.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.69-1.7310.9992.0741.322860.4392.16981.5
1.73-1.7813.4081.8161.6927220.531.88799.8
1.78-1.8313.7941.2932.4626520.711.34299.9
1.83-1.8914.1981.062.6525560.7661.09899.7
1.89-1.9513.6680.8943.7425210.7940.92899.8
1.95-2.0214.1550.5994.7424000.9060.62199.9
2.02-2.0913.7630.545.9223210.9150.56199.8
2.09-2.1814.7610.3537.6922910.9690.366100
2.18-2.2814.6760.3478.7121420.9660.36100
2.28-2.3916.6240.25411.9420960.9880.262100
2.39-2.5218.2960.21814.719840.990.224100
2.52-2.6718.6150.17916.5318650.9930.184100
2.67-2.8517.880.1618.217640.9950.165100
2.85-3.0817.7170.12421.5716700.9970.128100
3.08-3.3817.2080.09825.0115140.9970.101100
3.38-3.7715.6090.08727.2513930.9980.09100
3.77-4.3614.4150.07829.1512640.9980.081100
4.36-5.3416.1650.06737.5710460.9990.069100
5.34-7.5517.7250.05742.268480.9990.058100
7.55-45.71817.1760.04246.675120.9990.04499

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.67 Å45.72 Å
Translation3.67 Å45.72 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LP9

5lp9


Resolution: 1.69→45.718 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.2416 1908 5 %
Rwork0.1766 --
obs0.1799 38168 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.3 Å2 / Biso mean: 42.684 Å2 / Biso min: 18.73 Å2
Refinement stepCycle: final / Resolution: 1.69→45.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 21 221 2483
Biso mean--63.55 48.49 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092284
X-RAY DIFFRACTIONf_angle_d0.8593134
X-RAY DIFFRACTIONf_chiral_restr0.058399
X-RAY DIFFRACTIONf_plane_restr0.006414
X-RAY DIFFRACTIONf_dihedral_angle_d8.8311351
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1584X-RAY DIFFRACTION7.404TORSIONAL
12B1584X-RAY DIFFRACTION7.404TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.69-1.73230.42241340.298625522686
1.7323-1.77910.35141340.276925512685
1.7791-1.83150.3481340.249625592693
1.8315-1.89060.34551330.223925182651
1.8906-1.95820.2921360.204225962732
1.9582-2.03660.25441340.161925442678
2.0366-2.12920.23511340.149725452679
2.1292-2.24150.22491360.134825802716
2.2415-2.38190.22621360.144325832719
2.3819-2.56580.22071360.144225782714
2.5658-2.8240.24441370.156526032740
2.824-3.23250.23221390.154526362775
3.2325-4.07230.19121380.153926322770
4.0723-45.73420.25141470.215227832930

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