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- PDB-6r5w: Crystal structure of the receptor binding protein (gp15) of Liste... -

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Basic information

Entry
Database: PDB / ID: 6r5w
TitleCrystal structure of the receptor binding protein (gp15) of Listeria phage PSA
ComponentsGp15 protein
KeywordsVIRAL PROTEIN / Listeria / homotrimeric / receptor binding protein / Bacteriophage
Function / homologyBppU, N-terminal / BppU N-terminal domain / ACETATE ION / : / Gp15 protein
Function and homology information
Biological speciesListeria phage PSA (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsDunne, M. / Ernst, P. / Pluckthun, A. / Loessner, M.J. / Kilcher, S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationSNF_174108 Switzerland
CitationJournal: Cell Rep / Year: 2019
Title: Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins.
Authors: Dunne, M. / Rupf, B. / Tala, M. / Qabrati, X. / Ernst, P. / Shen, Y. / Sumrall, E. / Heeb, L. / Pluckthun, A. / Loessner, M.J. / Kilcher, S.
History
DepositionMar 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp15 protein
B: Gp15 protein
C: Gp15 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,06316
Polymers54,4573
Non-polymers1,60613
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-135 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.700, 134.700, 79.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21C-614-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATHRTHR(chain 'A' and (resid 203 through 228 or resid 230...AA203 - 2283 - 28
12TRPTRPLEULEU(chain 'A' and (resid 203 through 228 or resid 230...AA230 - 25630 - 56
13SERSERSERSER(chain 'A' and (resid 203 through 228 or resid 230...AA25858
14VALVALTYRTYR(chain 'A' and (resid 203 through 228 or resid 230...AA260 - 32460 - 124
15ALAALAGLUGLU(chain 'A' and (resid 203 through 228 or resid 230...AA326 - 370126 - 170
26ALAALATHRTHR(chain 'B' and (resid 203 through 228 or resid 230...BB203 - 2283 - 28
27TRPTRPLEULEU(chain 'B' and (resid 203 through 228 or resid 230...BB230 - 25630 - 56
28SERSERSERSER(chain 'B' and (resid 203 through 228 or resid 230...BB25858
29VALVALTYRTYR(chain 'B' and (resid 203 through 228 or resid 230...BB260 - 32460 - 124
210ALAALAGLUGLU(chain 'B' and (resid 203 through 228 or resid 230...BB326 - 370126 - 170
311ALAALATHRTHR(chain 'C' and (resid 203 through 228 or resid 230...CC203 - 2283 - 28
312TRPTRPLEULEU(chain 'C' and (resid 203 through 228 or resid 230...CC230 - 25630 - 56
313SERSERSERSER(chain 'C' and (resid 203 through 228 or resid 230...CC25858
314VALVALTYRTYR(chain 'C' and (resid 203 through 228 or resid 230...CC260 - 32460 - 124
315ALAALAGLUGLU(chain 'C' and (resid 203 through 228 or resid 230...CC326 - 370126 - 170

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Components

#1: Protein Gp15 protein


Mass: 18152.275 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria phage PSA (virus) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8W5Z4
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Na Acetate, pH 4.6, 30% (v/v) PEG 400, and 0.1 M Cadmium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→44.09 Å / Num. obs: 91053 / % possible obs: 99.95 % / Redundancy: 10.2 % / Biso Wilson estimate: 31.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07093 / Rpim(I) all: 0.02333 / Rrim(I) all: 0.07473 / Net I/σ(I): 17.76
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 2.323 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 8999 / CC1/2: 0.386 / Rpim(I) all: 0.7629 / Rrim(I) all: 2.447 / % possible all: 99.98

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Processing

Software
NameClassification
REFMACrefinement
PHENIXrefinement
XDSdata scaling
SHELXDEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→44.09 Å / SU ML: 0.2387 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 24.4971
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 8862 5 %4555
Rwork0.1907 ---
obs0.1917 177095 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 49 493 4300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01653880
X-RAY DIFFRACTIONf_angle_d1.2315278
X-RAY DIFFRACTIONf_chiral_restr0.0776635
X-RAY DIFFRACTIONf_plane_restr0.0086677
X-RAY DIFFRACTIONf_dihedral_angle_d12.76122304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.38012960.34715602X-RAY DIFFRACTION99.95
1.72-1.740.34882960.34035552X-RAY DIFFRACTION99.93
1.74-1.760.34982880.32825629X-RAY DIFFRACTION100
1.76-1.780.34362970.34135588X-RAY DIFFRACTION99.98
1.78-1.810.34442970.33935629X-RAY DIFFRACTION99.85
1.81-1.830.33292960.32365594X-RAY DIFFRACTION99.92
1.83-1.860.33182980.30195588X-RAY DIFFRACTION99.24
1.86-1.890.29892880.28725677X-RAY DIFFRACTION100
1.89-1.910.29742970.26625517X-RAY DIFFRACTION100
1.91-1.950.25592960.25155660X-RAY DIFFRACTION99.95
1.95-1.980.27982960.24925651X-RAY DIFFRACTION100
1.98-2.020.26932880.23125539X-RAY DIFFRACTION100
2.02-2.050.25212950.23285649X-RAY DIFFRACTION100
2.05-2.10.25892980.22215611X-RAY DIFFRACTION100
2.1-2.140.24242960.21195655X-RAY DIFFRACTION100
2.14-2.190.22532930.20225570X-RAY DIFFRACTION99.97
2.19-2.250.24472910.19295574X-RAY DIFFRACTION100
2.25-2.310.20522950.1995627X-RAY DIFFRACTION99.98
2.31-2.380.2292950.19245624X-RAY DIFFRACTION100
2.38-2.450.24012970.19645630X-RAY DIFFRACTION100
2.45-2.540.21922990.18925621X-RAY DIFFRACTION100
2.54-2.640.20322970.18025584X-RAY DIFFRACTION99.59
2.64-2.760.18812930.17535592X-RAY DIFFRACTION100
2.76-2.910.22442950.19355589X-RAY DIFFRACTION100
2.91-3.090.20992940.18875594X-RAY DIFFRACTION100
3.09-3.330.19032990.18665634X-RAY DIFFRACTION100
3.33-3.660.16412970.16975621X-RAY DIFFRACTION100
3.66-4.190.17433000.15195630X-RAY DIFFRACTION100
4.19-5.280.15132930.13245593X-RAY DIFFRACTION99.93
5.28-47.020.22423020.20195609X-RAY DIFFRACTION99.86

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