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- PDB-2co2: Salmonella enterica SafA pilin in complex with a 19-residue SafA ... -

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Basic information

Entry
Database: PDB / ID: 2co2
TitleSalmonella enterica SafA pilin in complex with a 19-residue SafA Nte peptide (F3A mutant)
Components
  • SAFA N-TERMINAL EXTENSION
  • SAFA PILUS SUBUNIT
KeywordsFIBRIL PROTEIN / PILUS SUBUNIT / FOLD COMPLEMENTATION
Function / homology
Function and homology information


Saf-pilin pilus formation protein / Saf-pilin pilus formation protein / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein
Similarity search - Component
Biological speciesSALMONELLA ENTERICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / Refinement description / Version format compliance
Revision 1.2May 1, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAFA PILUS SUBUNIT
B: SAFA N-TERMINAL EXTENSION


Theoretical massNumber of molelcules
Total (without water)15,1312
Polymers15,1312
Non-polymers00
Water34219
1
A: SAFA PILUS SUBUNIT
B: SAFA N-TERMINAL EXTENSION

A: SAFA PILUS SUBUNIT
B: SAFA N-TERMINAL EXTENSION


Theoretical massNumber of molelcules
Total (without water)30,2624
Polymers30,2624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+5/61
MethodPQS
Unit cell
Length a, b, c (Å)68.499, 68.499, 130.567
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2003-

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: 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 ENTERICA (bacteria) / Strain: LT2 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q8ZRK4
#2: Protein/peptide SAFA N-TERMINAL EXTENSION


Mass: 1994.141 Da / Num. of mol.: 1 / Fragment: N-TERMINAL EXTENSION, RESIDUES 27-45 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SALMONELLA ENTERICA (bacteria) / References: UniProt: Q8ZRK4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, PHE 29 TO ALA

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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: 3.04 Å3/Da / Density % sol: 59.18 %
Crystal growpH: 4.6 / Details: pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 15190 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 43.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAFA ANTE WT

Resolution: 2.3→19.93 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.898 / SU B: 13.619 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 416 5 %RANDOM
Rwork0.23 ---
obs0.232 7983 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 0 19 1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221035
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9521408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0925.89739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08115174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.385154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02755
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2352
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.2685
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7051.5691
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26521096
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9793389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1874.5312
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 34
Rwork0.274 566
Refinement TLS params.Method: refined / Origin x: 24.949 Å / Origin y: -11.683 Å / Origin z: 42.148 Å
111213212223313233
T-0.0874 Å2-0.0058 Å2-0.022 Å2--0.0092 Å2-0.0744 Å2---0.0713 Å2
L2.3789 °21.5566 °2-0.655 °2-3.9952 °2-0.4642 °2--1.0975 °2
S0.0309 Å °0.2786 Å °-0.444 Å °0.145 Å °0.0684 Å °-0.3309 Å °-0.1677 Å °-0.0017 Å °-0.0992 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B4 - 19
2X-RAY DIFFRACTION1A23 - 143

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