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- PDB-2co6: Salmonella enterica SafA pilin in complex with the SafB chaperone... -

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Basic information

Entry
Database: PDB / ID: 2co6
TitleSalmonella enterica SafA pilin in complex with the SafB chaperone (Type I)
Components
  • PUTATIVE FIMBRIAE ASSEMBLY CHAPERONE
  • PUTATIVE OUTER MEMBRANE PROTEIN
KeywordsFIBRIL PROTEIN / PILUS SUBUNIT / ADHESION / STRAND COMPLEMENTATION / PATHOGENESIS / CHAPERONE
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: 2 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 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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: PUTATIVE OUTER MEMBRANE PROTEIN
B: PUTATIVE FIMBRIAE ASSEMBLY CHAPERONE


Theoretical massNumber of molelcules
Total (without water)37,1602
Polymers37,1602
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)115.370, 40.822, 65.946
Angle α, β, γ (deg.)90.00, 106.85, 90.00
Int Tables number5
Space group name H-MC121
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 PUTATIVE OUTER MEMBRANE PROTEIN / SAFA PILUS SUBUNIT


Mass: 13136.663 Da / Num. of mol.: 1 / Fragment: CORE PILIN DOMAIN, NTE DELETED, RESIDUES 48-170
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.1 %
Crystal growpH: 8.5
Details: 30% PEG 4000, 100 MM TRIS-HCL PH8.5, 200 MM SODIUM ACETATE, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.0726
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0726 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 20162 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4 / % possible all: 100

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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: 2→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.822 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1026 5.1 %RANDOM
Rwork0.181 ---
obs0.183 19127 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: 24.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å21.19 Å2
2--0.13 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 198 2716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222594
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9673543
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4695336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75224.95101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74415421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9831512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021950
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21128
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21729
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8771.51711
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45322716
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.33331003
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7384.5824
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 65
Rwork0.201 1421
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)
11.56440.66340.28391.26120.60880.6106-0.0252-0.1589-0.02080.07330.0145-0.01350.08780.03280.0107-0.01160.0066-0.0111-0.01010.0067-0.078759.4255.83621.774
20.39680.3946-0.20080.67740.02960.5422-0.05760.04120.0491-0.05490.08090.01480.0252-0.0252-0.0233-0.0046-0.0093-0.0142-0.03440.0085-0.025747.8186.362.857
31.81930.2217-0.85091.5015-1.02842.6318-0.008-0.12190.03480.06330.13970.1177-0.00120.0544-0.1317-0.03660.0018-0.0107-0.03950.0114-0.035732.21-13.39714.34
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 144
2X-RAY DIFFRACTION2B5 - 133
3X-RAY DIFFRACTION3B138 - 220

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