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- PDB-1yu3: Major Tropism Determinant I1 Variant -

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Basic information

Entry
Database: PDB / ID: 1yu3
TitleMajor Tropism Determinant I1 Variant
ComponentsMajor Tropism Determinant (Mtd-I1)
KeywordsVIRAL PROTEIN / C-type Lectin / Beta Sandwich / Beta Prism / variability / diversity-generating retroelement
Function / homology
Function and homology information


viral tropism switching / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell
Similarity search - Function
Seminal Fluid Protein PDC-109 (Domain B) - #30 / Tail fiber receptor-binding protein / Tail fiber receptor-binding protein / : / Mtd second domain / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / Sulfatase-modifying factor enzyme superfamily ...Seminal Fluid Protein PDC-109 (Domain B) - #30 / Tail fiber receptor-binding protein / Tail fiber receptor-binding protein / : / Mtd second domain / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / Sulfatase-modifying factor enzyme superfamily / Seminal Fluid Protein PDC-109 (Domain B) / C-type lectin fold / Trefoil / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tail fiber receptor-binding protein
Similarity search - Component
Biological speciesBordetella phage BIP-1 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsMcMahon, S.A. / Miller, J.L. / Lawton, J.A. / Ghosh, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The C-type lectin fold as an evolutionary solution for massive sequence variation
Authors: McMahon, S.A. / Miller, J.L. / Lawton, J.A. / Kerkow, D.E. / Hodes, A. / Marti-Renom, M.A. / Doulatov, S. / Narayanan, E. / Sali, A. / Miller, J.F. / Ghosh, P.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The author states there is an error in the database sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major Tropism Determinant (Mtd-I1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6122
Polymers39,5871
Non-polymers241
Water2,954164
1
A: Major Tropism Determinant (Mtd-I1)
hetero molecules

A: Major Tropism Determinant (Mtd-I1)
hetero molecules

A: Major Tropism Determinant (Mtd-I1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8356
Polymers118,7623
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area14540 Å2
ΔGint-90 kcal/mol
Surface area34560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.308, 92.308, 102.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-382-

MG

21A-461-

HOH

31A-472-

HOH

41A-480-

HOH

51A-491-

HOH

DetailsThe biological assembly is a trimer generated from: -y, x-y, z and -x+y, -x, z

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Components

#1: Protein Major Tropism Determinant (Mtd-I1)


Mass: 39587.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella phage BIP-1 (virus) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q775D6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.1 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: Isopropanol, Sodium Citrate, HEPES, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5479 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5479 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. all: 16724 / Num. obs: 16724 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.52→2.61 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YU0

1yu0


Resolution: 2.52→25.94 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.437 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21304 849 5.1 %RANDOM
Rwork0.17042 ---
all0.17254 16724 --
obs0.17254 16724 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.307 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.52→25.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 1 164 2924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0131.9063858
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84623.675117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56715378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9721512
X-RAY DIFFRACTIONr_chiral_restr0.070.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21315
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21953
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.2103
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2961.51866
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.55422919
X-RAY DIFFRACTIONr_scbond_it0.85831115
X-RAY DIFFRACTIONr_scangle_it1.3724.5939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.522→2.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 64 -
Rwork0.266 1140 -
obs--99.26 %

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