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- PDB-4bwr: Crystal structure of c5321: a protective antigen present in uropa... -

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Basic information

Entry
Database: PDB / ID: 4bwr
TitleCrystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold
ComponentsPROTEIN CORRESPONDING TO LOCUS C5321 FROM CFT073 E.COLI STRAIN
KeywordsUNKNOWN FUNCTION / SEL1-LIKE REPEAT / SUPER-HELICAL FOLD
Function / homology
Function and homology information


negative regulation of neutrophil activation / IgA binding / negative regulation of immune response / : / cell surface / metal ion binding
Similarity search - Function
Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Secretory immunoglobulin A-binding protein EsiB / Secretory immunoglobulin A-binding protein EsiB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsUrosev, D. / Ferrer-Navarro, M. / Pastorello, I. / Cartocci, E. / Costenaro, L. / Zhulenkovs, D. / Marechal, J.-D. / Leonchiks, A. / Reverter, D. / Serino, L. ...Urosev, D. / Ferrer-Navarro, M. / Pastorello, I. / Cartocci, E. / Costenaro, L. / Zhulenkovs, D. / Marechal, J.-D. / Leonchiks, A. / Reverter, D. / Serino, L. / Soriani, M. / Daura, X.
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: Crystal Structure of C5321: A Protective Antigen Present in Uropathogenic Escherichia Coli Strains Displaying an Slr Fold.
Authors: Urosev, D. / Ferrer-Navarro, M. / Pastorello, I. / Cartocci, E. / Costenaro, L. / Zhulenkovs, D. / Marechal, J. / Leonchiks, A. / Reverter, D. / Serino, L. / Soriani, M. / Daura, X.
History
DepositionJul 4, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionJul 24, 2013ID: 2XM6
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN CORRESPONDING TO LOCUS C5321 FROM CFT073 E.COLI STRAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,90333
Polymers53,0071
Non-polymers1,89532
Water8,395466
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.940, 58.520, 88.350
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN CORRESPONDING TO LOCUS C5321 FROM CFT073 E.COLI STRAIN


Mass: 53007.336 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-490
Source method: isolated from a genetically manipulated source
Details: PROTEIN CONTAINING SEL1-LIKE REPEATS / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: CFT073 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: Q8FAG2, UniProt: A0A0H2VDN9*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.23 Å3/Da / Density % sol: 44.8 % / Description: NONE
Crystal growpH: 8.5
Details: 20% PEG3350, 100 MM TRIS-HCL PH 8.5, AND 200 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9791 , 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2010 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
ReflectionResolution: 1.74→37.91 Å / Num. obs: 49642 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Biso Wilson estimate: 17.06 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.74→36.891 Å / SU ML: 0.16 / σ(F): 1.13 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 4928 5.1 %
Rwork0.1551 --
obs0.1569 49623 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.45 Å2
Refinement stepCycle: LAST / Resolution: 1.74→36.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 119 466 4291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064071
X-RAY DIFFRACTIONf_angle_d0.8845462
X-RAY DIFFRACTIONf_dihedral_angle_d14.4631554
X-RAY DIFFRACTIONf_chiral_restr0.05536
X-RAY DIFFRACTIONf_plane_restr0.003721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.75980.25421650.25413059X-RAY DIFFRACTION99
1.7598-1.78050.28181660.22792987X-RAY DIFFRACTION99
1.7805-1.80220.2561650.21953065X-RAY DIFFRACTION99
1.8022-1.8250.23121750.22443103X-RAY DIFFRACTION99
1.825-1.8490.25851400.21293038X-RAY DIFFRACTION99
1.849-1.87440.28171490.21373122X-RAY DIFFRACTION99
1.8744-1.90110.23051860.20333042X-RAY DIFFRACTION99
1.9011-1.92950.21381860.19983005X-RAY DIFFRACTION99
1.9295-1.95970.22811810.18383161X-RAY DIFFRACTION99
1.9597-1.99180.2171710.17632961X-RAY DIFFRACTION99
1.9918-2.02610.21241600.16723090X-RAY DIFFRACTION99
2.0261-2.0630.21691730.15723046X-RAY DIFFRACTION99
2.063-2.10260.22351590.14633042X-RAY DIFFRACTION99
2.1026-2.14560.17841470.13843132X-RAY DIFFRACTION100
2.1456-2.19220.19611850.13973085X-RAY DIFFRACTION100
2.1922-2.24320.2061710.13843089X-RAY DIFFRACTION100
2.2432-2.29930.16361540.13113053X-RAY DIFFRACTION99
2.2993-2.36140.19031270.13183102X-RAY DIFFRACTION99
2.3614-2.43090.18321640.13283080X-RAY DIFFRACTION99
2.4309-2.50940.18161820.13323020X-RAY DIFFRACTION100
2.5094-2.5990.20641670.13673112X-RAY DIFFRACTION100
2.599-2.70310.19541660.13313072X-RAY DIFFRACTION99
2.7031-2.8260.16891750.13943086X-RAY DIFFRACTION100
2.826-2.9750.20941850.15013000X-RAY DIFFRACTION99
2.975-3.16130.18351350.14623134X-RAY DIFFRACTION100
3.1613-3.40520.17081660.14313099X-RAY DIFFRACTION100
3.4052-3.74760.16971340.1433061X-RAY DIFFRACTION99
3.7476-4.28920.14871790.13493041X-RAY DIFFRACTION98
4.2892-5.40120.16511940.15243017X-RAY DIFFRACTION98
5.4012-36.89920.20651210.19313106X-RAY DIFFRACTION99

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