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- PDB-5lnd: Crystal structure of self-complemented MyfA, the major subunit of... -

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Basic information

Entry
Database: PDB / ID: 5lnd
TitleCrystal structure of self-complemented MyfA, the major subunit of Myf fimbriae from Yersinia enterocolitica
ComponentsFimbrial protein MyfA,Fimbrial protein MyfA,Fimbrial protein MyfA
KeywordsCELL ADHESION / Ig-like fold / beta sandwich / donor-strand complementation
Function / homologyImmunoglobulin-like - #3590 / : / : / Ph 6 antigen / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / Fimbrial protein MyfA
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / SAD / Resolution: 1.46 Å
AuthorsPakharukova, N.A. / Roy, S. / Tuitilla, M. / Zavialov, A.V.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland140959 Finland
Academy of Finland273075 Finland
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Structural basis for Myf and Psa fimbriae-mediated tropism of pathogenic strains of Yersinia for host tissues.
Authors: Pakharukova, N. / Roy, S. / Tuittila, M. / Rahman, M.M. / Paavilainen, S. / Ingars, A.K. / Skaldin, M. / Lamminmaki, U. / Hard, T. / Teneberg, S. / Zavialov, A.V.
History
DepositionAug 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: Fimbrial protein MyfA,Fimbrial protein MyfA,Fimbrial protein MyfA
B: Fimbrial protein MyfA,Fimbrial protein MyfA,Fimbrial protein MyfA


Theoretical massNumber of molelcules
Total (without water)29,2862
Polymers29,2862
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint1 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.970, 41.979, 151.185
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fimbrial protein MyfA,Fimbrial protein MyfA,Fimbrial protein MyfA / C-AG / Myf antigen


Mass: 14642.776 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: myfA / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P33406
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.3 Å3/Da / Density % sol: 46.52 % / Mosaicity: 0.18 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 35% dioxane v/v

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.43
ReflectionResolution: 1.46→41.979 Å / Num. all: 45504 / Num. obs: 45504 / % possible obs: 96.7 % / Redundancy: 3.3 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Rsym value: 0.063 / Net I/av σ(I): 5.094 / Net I/σ(I): 10.1 / Num. measured all: 149827
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.46-1.513.30.4741.61511545150.2920.5610.4742.298.7
1.51-1.573.30.3292.41430643610.2030.3890.3293.298.6
1.57-1.633.20.25431307940950.1560.3010.2544.196.9
1.63-1.73.20.1983.91286739900.1220.2340.1985.397.9
1.7-1.793.40.1475.21300238440.0880.1720.1477.498.7
1.79-1.883.40.1146.61231736560.0670.1330.1149.798
1.88-23.30.0927.91141734540.0540.1070.09212.296.5
2-2.143.10.0759.6959131180.0470.0890.07513.994.9
2.14-2.313.40.0719.71017629820.0410.0820.0711697
2.31-2.533.40.06710.3922627490.0390.0780.06716.396.5
2.53-2.833.30.06410.5816324860.0370.0750.06416.894.4
2.83-3.263.20.0639.9681721330.0370.0730.06317.493.2
3.26-43.40.05611.6630418500.0320.0650.05618.494.4
4-5.653.20.05111.2460614190.0310.060.0511891.7
5.65-41.9793.30.04910.628418520.0290.0570.0491892.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.46→40.449 Å / FOM work R set: 0.7612 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.61 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1936 2356 5.18 %
Rwork0.1806 43152 -
obs0.1853 45478 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.08 Å2 / Biso mean: 23.09 Å2 / Biso min: 12.94 Å2
Refinement stepCycle: final / Resolution: 1.46→40.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 0 250 2194
Biso mean---27.91 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071983
X-RAY DIFFRACTIONf_angle_d0.9962684
X-RAY DIFFRACTIONf_chiral_restr0.067289
X-RAY DIFFRACTIONf_plane_restr0.003353
X-RAY DIFFRACTIONf_dihedral_angle_d14.259692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4602-1.49190.35621630.3572728289193
1.4919-1.52660.31541460.31752684283093
1.5266-1.56480.31961530.31022757291093
1.5648-1.60710.26591540.30352674282892
1.6071-1.65440.29431390.29512616275590
1.6544-1.70780.30281470.27672733288093
1.7078-1.76880.26921620.26142729289193
1.7688-1.83960.21611430.24162752289593
1.8396-1.92340.22291420.23292682282492
1.9234-2.02480.23521380.20942642278090
2.0248-2.15160.19471340.19852655278990
2.1516-2.31770.18681190.1922750286992
2.3177-2.55080.18971500.19362672282290
2.5508-2.91970.18321460.18352619276587
2.9197-3.67770.16571430.13942695283888
3.6777-32.26230.16021250.12542764288986

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