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- PDB-2xet: Conserved hydrophobic clusters on the surface of the Caf1A usher ... -

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Basic information

Entry
Database: PDB / ID: 2xet
TitleConserved hydrophobic clusters on the surface of the Caf1A usher C-terminal domain are important for F1 antigen assembly
ComponentsF1 CAPSULE-ANCHORING PROTEIN
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell outer membrane
Similarity search - Function
PapC, C-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain ...PapC, C-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
F1 capsule-anchoring protein
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsDubnovitsky, A.P. / Duck, Z. / Kersley, J.E. / Hard, T. / MacIntyre, S. / Knight, S.D.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Conserved Hydrophobic Clusters on the Surface of the Caf1A Usher C-Terminal Domain are Important for F1 Antigen Assembly.
Authors: Dubnovitsky, A.P. / Duck, Z. / Kersley, J.E. / Hard, T. / Macintyre, S. / Knight, S.D.
History
DepositionMay 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F1 CAPSULE-ANCHORING PROTEIN
B: F1 CAPSULE-ANCHORING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3885
Polymers19,1002
Non-polymers2883
Water3,999222
1
A: F1 CAPSULE-ANCHORING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7423
Polymers9,5501
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: F1 CAPSULE-ANCHORING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6462
Polymers9,5501
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.669, 40.336, 44.862
Angle α, β, γ (deg.)90.00, 92.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.996248, 0.006666, 0.086282), (0.007386, -0.99994, -0.008028), (0.086223, 0.008635, -0.996238)
Vector: -1.0169, -3.4967, 19.2632)

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Components

#1: Protein F1 CAPSULE-ANCHORING PROTEIN / CAF1A USHER


Mass: 9549.886 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 745-833
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: P26949
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.84 Å3/Da / Density % sol: 33 % / Description: NONE
Crystal growpH: 3
Details: 0.2M LISO4, 12-15% PEG8000, 4% PEG400, 0.1M NA-CITRATE PH2.8-3.0, PROTEIN 15 G/L, MIXED 1:1, MICROSEEDING

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID23-111.069
SYNCHROTRONESRF ID14-220.933
Detector
TypeIDDetectorDate
ADSC CCD1CCDJun 28, 2008
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0691
20.9331
ReflectionResolution: 1.6→40 Å / Num. obs: 17753 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / % possible all: 80.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.957 / SU B: 1.319 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 915 5.2 %RANDOM
Rwork0.167 ---
obs0.1678 17742 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20.12 Å2
2---0.89 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 15 222 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221370
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9911850
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4735175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.624.04347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85815252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.337158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02980
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2516
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2936
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.5904
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3621420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1033530
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3014.5430
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 0 -
Rwork0.263 961 -
obs--69.94 %

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