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- PDB-2co7: Salmonella enterica SafA pilin in complex with the SafB chaperone... -

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Basic information

Entry
Database: PDB / ID: 2co7
TitleSalmonella enterica SafA pilin in complex with the SafB chaperone (Type II)
Components
  • PUTATIVE FIMBRIAE ASSEMBLY CHAPERONE
  • SAFA PILUS SUBUNIT
KeywordsFIBRIL PROTEIN / PILUS SUBUNIT / CHAPERONE / ADHESION / STRAND COMPLEMENTATION / PATHOGENESIS
Function / homology
Function and homology information


: / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
Saf-pilin pilus formation protein / Saf-pilin pilus formation protein / Dr adhesin / Dr-adhesin superfamily / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. ...Saf-pilin pilus formation protein / Saf-pilin pilus formation protein / Dr adhesin / Dr-adhesin superfamily / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fimbriae assembly chaparone / Outer membrane protein
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRemaut, H. / Rose, R.J. / Hannan, T.J. / Hultgren, S.J. / Radford, S.E. / Ashcroft, A.E. / Waksman, G.
CitationJournal: Mol.Cell / Year: 2006
Title: Donor-Strand Exchange in Chaperone-Assisted Pilus Assembly Proceeds Through a Concerted Beta-Strand Displacement Mechanism
Authors: Remaut, H. / Rose, R.J. / Hannan, T.J. / Hultgren, S.J. / Radford, S.E. / Ashcroft, A.E. / Waksman, G.
History
DepositionMay 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.3Dec 13, 2023Group: 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAFA PILUS SUBUNIT
B: PUTATIVE FIMBRIAE ASSEMBLY CHAPERONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5774
Polymers37,3852
Non-polymers1922
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.388, 40.595, 72.039
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2055-

HOH

21B-2066-

HOH

DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350THE N-TERMINAL EXTENSION PEPTIDE OF ONE SUBUNIT, CHAIN B,INSERTS INTO THE FOLD OF ANOTHER, CHAIN A. THIS INTERACTIONIS REPETED IN THE POLYMER, AN N-TERMINAL EXTENSION OFMOLECULE C WOULD INSERT IN TO THE SUBUNIT OF MOLECULE B , DINTO C ETC

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Components

#1: Protein SAFA PILUS SUBUNIT


Mass: 13361.907 Da / Num. of mol.: 1 / Fragment: CORE PILIN DOMAIN, NTE DELETED, RESIDUES 46-170 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Strain: LT2 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q8ZRK4
#2: Protein PUTATIVE FIMBRIAE ASSEMBLY CHAPERONE / SAFB CHAPERONE


Mass: 24023.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Strain: LT2 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q8ZRK3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES IN THE NTD OF CHAIN A WERE DELETED IN THE SAMPLE USED IN THE EXPERIMENT.

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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: 2.22 Å3/Da / Density % sol: 44.2 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 20% PEG 4000, 200 MM AMMONIUM ACETATE, 10% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 27689 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.3 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L4I

1l4i


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.695 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1379 5 %RANDOM
Rwork0.19 ---
obs0.192 26305 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20.25 Å2
2---0.71 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 10 274 2644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222455
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9693359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4425316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52824.74297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63615397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9491512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021830
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21129
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21634
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8641.51602
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38322545
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1793973
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.414.5807
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 113
Rwork0.215 1877
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.00380.22930.0312.0122-0.0250.4210.0070.03330.0438-0.0448-0.0094-0.1482-0.05820.04560.0025-0.1395-0.0090.0107-0.14220.0079-0.121946.58688.8692.1728
22.26070.0073-0.77592.8373-0.05331.97740.0247-0.5054-0.03030.46530.06940.21150.0582-0.0388-0.0942-0.0738-0.00330.0193-0.05030.0195-0.073931.3459-10.23913.6336
31.2410.11470.70071.85770.49723.523-0.0512-0.27550.12370.24390.0133-0.1658-0.08490.52780.038-0.0167-0.0344-0.01170.08550.002-0.104757.14668.069122.1285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B8 - 133
2X-RAY DIFFRACTION2B138 - 221
3X-RAY DIFFRACTION3A20 - 144

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