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- PDB-2iou: Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bord... -

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Basic information

Entry
Database: PDB / ID: 2iou
TitleMajor Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella brochiseptica Virulence Factor Pertactin extracellular domain (Prn-E).
Components
  • Major Tropism Determinant P1
  • Pertactin Extracellular Domain
Keywordsviral protein/membrane protein / Mtd / Prn / pertactin / viral protein-membrane protein COMPLEX
Function / homology
Function and homology information


viral tropism switching / virus tail, fiber / outer membrane / adhesion receptor-mediated virion attachment to host cell / : / cell outer membrane / membrane => GO:0016020 / periplasmic space / cell adhesion / symbiont entry into host cell ...viral tropism switching / virus tail, fiber / outer membrane / adhesion receptor-mediated virion attachment to host cell / : / cell outer membrane / membrane => GO:0016020 / periplasmic space / cell adhesion / symbiont entry into host cell / cell surface / extracellular region
Similarity search - Function
Pertactin autotransporter / Seminal Fluid Protein PDC-109 (Domain B) - #30 / Tail fiber receptor-binding protein / Tail fiber receptor-binding protein / Pertactin virulence factor family / Pertactin, central region / Pertactin / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / paralog of FGE (formylglycine-generating enzyme) ...Pertactin autotransporter / Seminal Fluid Protein PDC-109 (Domain B) - #30 / Tail fiber receptor-binding protein / Tail fiber receptor-binding protein / Pertactin virulence factor family / Pertactin, central region / Pertactin / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / Pectate Lyase C-like - #20 / Sulfatase-modifying factor enzyme superfamily / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Seminal Fluid Protein PDC-109 (Domain B) / Pectate Lyase C-like / Pectin lyase fold/virulence factor / 3 Solenoid / C-type lectin fold / Trefoil / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pertactin autotransporter / Pertactin / Tail fiber receptor-binding protein
Similarity search - Component
Biological speciesBordetella phage BPP-1 (virus)
Bordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsMiller, J.L. / Ghosh, P.
CitationJournal: Plos Biol. / Year: 2008
Title: Selective Ligand Recognition by a Diversity-Generating Retroelement Variable Protein
Authors: Miller, J.L. / Le Coq, J. / Hodes, A. / Barbalat, R. / Miller, J.F. / Ghosh, P.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Major Tropism Determinant P1
B: Major Tropism Determinant P1
C: Major Tropism Determinant P1
D: Major Tropism Determinant P1
E: Major Tropism Determinant P1
F: Major Tropism Determinant P1
G: Pertactin Extracellular Domain
H: Pertactin Extracellular Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,29812
Polymers343,2018
Non-polymers974
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36020 Å2
ΔGint-243 kcal/mol
Surface area106280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)413.464, 413.464, 98.859
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Major Tropism Determinant P1 / Phage tail protein


Mass: 39037.918 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella phage BPP-1 (virus) / Gene: Mtd / Plasmid: pet28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: Q775D6
#2: Protein Pertactin Extracellular Domain / Outer membrane protein P.68


Mass: 54486.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB50 / Gene: Prn / Plasmid: pet28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: Q03035, UniProt: Q3YE50*PLUS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2M NaCl, 200mM Lithium Sulfate, 100mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.156→50 Å / Num. obs: 166289 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 81.5 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 6
Reflection shellResolution: 3.156→3.26 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.467 / Cor.coef. Fo:Fc: 0.561 / Cor.coef. Io to Ic: 0.61
Highest resolutionLowest resolution
Rotation3.156 Å15 Å
Translation3.156 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YU0

1yu0


Resolution: 3.16→49.63 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.9 / SU B: 14.78 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.446 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24934 8362 5 %RANDOM
Rwork0.22405 ---
obs0.22533 157861 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.528 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.16→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23896 0 4 0 23900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02124430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.92233286
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14553262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68923.534996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.572153404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.52515140
X-RAY DIFFRACTIONr_chiral_restr0.0780.23728
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218950
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.211065
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.216457
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2707
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.050.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4081.516233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.747225432
X-RAY DIFFRACTIONr_scbond_it0.75839270
X-RAY DIFFRACTIONr_scangle_it1.3154.57854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.156→3.238 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 602 -
Rwork0.33 11518 -
obs--99.44 %

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