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- PDB-3fcg: Crystal Structure Analysis of the Middle Domain of the Caf1A Usher -

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Basic information

Entry
Database: PDB / ID: 3fcg
TitleCrystal Structure Analysis of the Middle Domain of the Caf1A Usher
ComponentsF1 capsule-anchoring protein
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / beta barrel / beta strand swapping / Cell membrane / Cell outer membrane / Cell projection / Fimbrium / Membrane / Plasmid / Transmembrane / Transport
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell outer membrane
Similarity search - Function
Outer membrane usher protein / 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 ...Outer membrane usher protein / 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 / SAD / Resolution: 2.85 Å
AuthorsYu, X. / Visweswaran, G.R. / Duck, Z. / Marupakula, S. / MacIntyre, S. / Knight, S. / Zavialov, A.V.
CitationJournal: Biochem.J. / Year: 2009
Title: Caf1A usher possesses a Caf1 subunit-like domain that is crucial for Caf1 fibre secretion
Authors: Yu, X. / Visweswaran, G.R. / Duck, Z. / Marupakula, S. / MacIntyre, S. / Knight, S.D. / Zavialov, A.V.
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)19,5863
Polymers19,5502
Non-polymers351
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-16 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.985, 111.966, 115.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1-

CL

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Components

#1: Protein F1 capsule-anchoring protein


Mass: 9775.033 Da / Num. of mol.: 2 / Fragment: Usher Middle Domain, UNP residues 253-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Plasmid: pCR-U232-320 / Production host: Escherichia coli (E. coli) / References: UniProt: P26949
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 8000, 0.2 M MgCl2, 0.1 M Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: Bruker XFlash / Detector: CCD / Date: Nov 26, 2007
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 5685 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 74.91 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 20.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.2 / Num. unique all: 792 / Rsym value: 0.573 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
SOLVEphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.85→20 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.885 / SU B: 17.955 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 2.668 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28694 221 4.6 %RANDOM
Rwork0.2644 ---
obs0.26544 4613 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.988 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---2.9 Å20 Å2
3---2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 1 6 1130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221153
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8471.9541581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0075142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21715157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.098156
X-RAY DIFFRACTIONr_chiral_restr0.0530.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02888
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1470.2360
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2741
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0790.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2021.5746
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.31621186
X-RAY DIFFRACTIONr_scbond_it0.3553467
X-RAY DIFFRACTIONr_scangle_it0.5154.5395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 22 -
Rwork0.411 328 -
obs--100 %

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