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- PDB-5lo7: Crystal structure of self-complemented MyfA, the major subunit of... -

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Basic information

Entry
Database: PDB / ID: 5lo7
TitleCrystal structure of self-complemented MyfA, the major subunit of Myf fimbriae from Yersinia enterocolitica
ComponentsFimbrial 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Jan 10, 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

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Assembly

Deposited unit
A: Fimbrial protein MyfA,Fimbrial protein MyfA
B: Fimbrial protein MyfA,Fimbrial protein MyfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2323
Polymers29,1112
Non-polymers1201
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint2 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.980, 41.970, 150.830
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 / C-AG / Myf antigen


Mass: 14555.698 Da / Num. of mol.: 2 / Fragment: UNP residues 51-159,UNP residues 30-47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: myfA / Plasmid: pET101D / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P33406
#2: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
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: BM14 / Wavelength: 0.9737 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.29
ReflectionResolution: 1.8→150.83 Å / Num. all: 25547 / Num. obs: 25547 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.099 / Rsym value: 0.085 / Net I/av σ(I): 6.869 / Net I/σ(I): 9.6 / Num. measured all: 94487
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
1.8-1.93.70.75811360336620.4470.8850.7581.8100
1.9-2.013.70.4231.81294234780.250.4940.4233.1100
2.01-2.153.70.2552.91208032450.1510.2980.2555.2100
2.15-2.323.70.174.41152530800.10.1990.177.4100
2.32-2.553.70.1285.81049028270.0750.1490.1288.9100
2.55-2.853.70.0888.1962725960.0520.1030.08812.1100
2.85-3.293.70.0669.7845322800.0380.0770.06617.199.9
3.29-4.023.70.05911718219560.0330.0680.05920.899.8
4.02-5.693.60.04114.9551415250.0240.0480.04122.299.5
5.69-29.6813.40.03217.330718980.0190.0380.03220.497.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
PHENIX1.8.2_1309model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LND

5lnd


Resolution: 1.9→29.681 Å / FOM work R set: 0.8083 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.82 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1912 1116 5.13 %
Rwork0.1587 20593 -
obs0.1623 21748 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.15 Å2 / Biso mean: 26.61 Å2 / Biso min: 10.05 Å2
Refinement stepCycle: final / Resolution: 1.9→29.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 20 305 2276
Biso mean--27.12 34.08 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121998
X-RAY DIFFRACTIONf_angle_d1.4312702
X-RAY DIFFRACTIONf_chiral_restr0.082291
X-RAY DIFFRACTIONf_plane_restr0.005354
X-RAY DIFFRACTIONf_dihedral_angle_d15.497697
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9008-1.98730.26111220.23512534265695
1.9873-2.09190.23141550.2092518267394
2.0919-2.22280.22491400.19722531267195
2.2228-2.39410.21311360.18672536267295
2.3941-2.63450.19671460.18922566271295
2.6345-3.01440.20581360.16832601273795
3.0144-3.79310.17531390.1382590272995
3.7931-19.18360.16431390.12332717285694

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