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- PDB-1n7v: THE RECEPTOR-BINDING PROTEIN P2 OF BACTERIOPHAGE PRD1: CRYSTAL FO... -

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Basic information

Entry
Database: PDB / ID: 1n7v
TitleTHE RECEPTOR-BINDING PROTEIN P2 OF BACTERIOPHAGE PRD1: CRYSTAL FORM III
ComponentsAdsorption protein P2
KeywordsVIRAL PROTEIN / bacteriophage PRD1 / viral receptor-binding / beta-propeller / proline-rich / antibiotic-resistance
Function / homology
Function and homology information


virion component / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
3 Propeller / Pseudo beta propeller / Pseudo beta propeller / receptor-binding protein prd1-p2, domain 2 / receptor-binding protein prd1-p2, domain 2 / receptor-binding protein prd1-p2, domain 3 / receptor-binding protein prd1-p2, domain 3 / Bacteriophage PRD1, P2, absorption protein / Bacteriophage PRD1, P2, C-terminal / Bacteriophage PRD1, P2, N-terminal ...3 Propeller / Pseudo beta propeller / Pseudo beta propeller / receptor-binding protein prd1-p2, domain 2 / receptor-binding protein prd1-p2, domain 2 / receptor-binding protein prd1-p2, domain 3 / receptor-binding protein prd1-p2, domain 3 / Bacteriophage PRD1, P2, absorption protein / Bacteriophage PRD1, P2, C-terminal / Bacteriophage PRD1, P2, N-terminal / Bacteriophage PRD1, P2, absorption protein superfamily / Bacteriophage Prd1, adsorption protein P2 / Distorted Sandwich / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Adsorption protein P2
Similarity search - Component
Biological speciesEnterobacteria phage PRD1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXu, L. / Benson, S.D. / Butcher, S.J. / Bamford, D.H. / Burnett, R.M.
Citation
Journal: Structure / Year: 2003
Title: The Receptor Binding Protein P2 of PRD1, a Virus Targeting Antibiotic-Resistant Bacteria, Has a Novel Fold Suggesting Multiple Functions.
Authors: Xu, L. / Benson, S.D. / Butcher, S.J. / Bamford, D.H. / Burnett, R.M.
#1: Journal: J.STRUCT.BIOL. / Year: 2000
Title: Crystallization and preliminary X-ray analysis of receptor-binding protein P2 of bacteriopahge PRD1
Authors: Xu, L. / Butcher, S.J. / Benson, S.D. / Bamford, D.H. / Burnett, R.M.
#2: Journal: J.BACTERIOL. / Year: 1999
Title: Stable packing of phage PRD1 DNA requires adsorption protein P2, which binds to the IncP plasmid-encoded conjugative transfer complex
Authors: Grahn, A.M. / Caldentey, J. / Bamford, J.K.H. / Bamford, D.H.
#3: Journal: Adv.Virus Res. / Year: 1995
Title: Bacteriophage PRD1: a broad host range dsDNA tectivirus with an internal membrane
Authors: Bamford, D.H. / Caldentey, J. / Bamford, J.K.H.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures
Authors: Benson, S.D. / Bamford, J.K.H. / Bamford, D.H. / Burnett, R.M.
#5: Journal: J.Mol.Biol. / Year: 1999
Title: Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex
Authors: Rydman, P.S. / Caldentey, J. / Butcher, S.J. / Fuller, S.D. / Rutten, T. / Bamford, D.H.
#6: Journal: Thesis / Year: 2002
Title: A tale of two viruses with therapeutic potential: Structural studies on CELO, an avian adenovirus and the bacteriophage PRD1
Authors: Xu, L.
History
DepositionNov 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 14, 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_initial_refinement_model / pdbx_struct_conn_angle / 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_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.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_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_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
Remark 351 The biomolecule is most probably a monomer. Nevertheless, it is notable that the same dimer ... The biomolecule is most probably a monomer. Nevertheless, it is notable that the same dimer appears in the two crystal forms (1N7U and 1N7V). Although the buried surface per subunit in the dimer is ~1,206 A**2, which is relatively substantial, it only represents ~5.5% of the surface area of the P2 monomer. Rate zonal centrifugation, gel filtration, cross-linking, sedimentation equilibrium and low angle X-ray scattering strongly suggest that P2 is a monomer in solution. Furthermore, dynamic light scattering measurements indicated a monodisperse solution with an apparent molecular weight of 79 kDa, which is in reasonable agreement with that for the monomer (63.9 kDa). Nevertheless, P2 may form a loosely associated dimer when bound to the virion.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adsorption protein P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0844
Polymers59,9251
Non-polymers1583
Water4,216234
1
A: Adsorption protein P2
hetero molecules

A: Adsorption protein P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1678
Polymers119,8512
Non-polymers3166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)46.500, 270.200, 137.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsBiochemical evidence (gel filtration, low angle X-ray scattering, rate-zonal ultracentrifugation, and dynamic light scattering) indicate that P2 is monomeric, but a potential dimer appears in 3 crystal with different space groups and is obtained for this crystal form by the following symmetry operation: -x, y, -z+1/2

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Components

#1: Protein Adsorption protein P2 / Receptor-binding protein PRD1-P2


Mass: 59925.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage PRD1 (virus) / Genus: Tectivirus / Gene: II / Plasmid: pMG59 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P27378
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.38 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop, macroseeding / pH: 5
Details: 50% MPD, 0.1 M sodium acetate at pH 5.0, 10 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, MACROSEEDING, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 %MPD1reservoir
20.1 Msodium acetate1reservoirpH5.0
310 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Jan 1, 2000 / Details: Mirrors
RadiationMonochromator: double-crystal monochromator si(111), beam focused by a toroidal mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.2→38 Å / Num. all: 44325 / Num. obs: 38750 / % possible obs: 87.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.6 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.064 / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.34 Å / Num. unique all: 3312 / Rsym value: 0.771 / % possible all: 45.1
Reflection
*PLUS
Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 58.7 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P2 Crystal Form I(1N7U)

1n7u


Resolution: 2.2→38.11 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1732 5 %RANDOM
Rwork0.229 ---
all0.243 44653 --
obs0.229 34808 78.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.6661 Å2 / ksol: 0.319657 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-30.77 Å20 Å20 Å2
2---17.45 Å20 Å2
3----13.32 Å2
Refine analyzeLuzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.51 Å
Refinement stepCycle: LAST / Resolution: 2.2→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 9 234 4234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.412 157 4.7 %
Rwork0.375 3155 -
obs--45.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ACY.PARACY.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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