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- PDB-3d8m: Crystal structure of a chimeric receptor binding protein from lac... -

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Basic information

Entry
Database: PDB / ID: 3d8m
TitleCrystal structure of a chimeric receptor binding protein from lactococcal phages subspecies TP901-1 and p2
ComponentsBaseplate protein, Receptor binding protein
KeywordsVIRUS/VIRAL PROTEIN / lactococcal phage p2 / lactococcal phage TP901-1 / receptor binding protein / VIRUS-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


virus tail, baseplate / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Helix Hairpins - #2190 / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Phage tail base-plate Siphoviridae RBP, head domain / : / Lactococcus phage p2, Receptor binding protein, neck domain / : / Lactophage receptor-binding protein N-terminal shoulder domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain ...Helix Hairpins - #2190 / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Phage tail base-plate Siphoviridae RBP, head domain / : / Lactococcus phage p2, Receptor binding protein, neck domain / : / Lactophage receptor-binding protein N-terminal shoulder domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Adenovirus pIV-like, attachment domain / Helix Hairpins / Helix non-globular / Special / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor binding protein / BPP
Similarity search - Component
Biological speciesLactococcus phage TP901-1 (virus)
Lactococcus phage p2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsSiponen, M.I. / Blangy, S. / Spinelli, S. / Cambillau, C. / Campanacci, V.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Crystal structure of a chimeric receptor binding protein constructed from two lactococcal phages
Authors: Siponen, M. / Spinelli, S. / Blangy, S. / Moineau, S. / Cambillau, C. / Campanacci, V.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baseplate protein, Receptor binding protein


Theoretical massNumber of molelcules
Total (without water)17,8721
Polymers17,8721
Non-polymers00
Water00
1
A: Baseplate protein, Receptor binding protein

A: Baseplate protein, Receptor binding protein

A: Baseplate protein, Receptor binding protein


Theoretical massNumber of molelcules
Total (without water)53,6163
Polymers53,6163
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area12860 Å2
ΔGint-55.4 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.833, 85.833, 85.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Baseplate protein, Receptor binding protein / BPP


Mass: 17872.090 Da / Num. of mol.: 1 / Fragment: UNP residues 1-62, UNP residues 162-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus), (gene. exp.) Lactococcus phage p2 (virus)
Strain: TP901-1, p2 / Gene: ORF49, ORF18 / Plasmid: pDEST17 O/I / Production host: Escherichia coli (E. coli) / Strain (production host): C41pLysRos / References: UniProt: Q9G096, UniProt: Q1RNF7

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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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Sodium Cacodylate, 12% MPEG2000, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2007 / Details: toroidal mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.35→85.75 Å / Num. all: 3206 / Num. obs: 3206 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 19.9 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.245 / Rsym value: 0.245 / Net I/σ(I): 15.9
Reflection shellResolution: 3.35→3.53 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 6.6 / Num. unique all: 450 / Rsym value: 0.509 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BSD, 2F0C

2bsd

2f0c


Resolution: 3.35→60.69 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.785 / SU B: 60.213 / SU ML: 0.425 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.623 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27437 450 14.1 %RANDOM
Rwork0.22108 ---
all0.22853 2744 --
obs0.22853 2744 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.928 Å2
Refine analyzeLuzzati coordinate error free: 0.623 Å
Refinement stepCycle: LAST / Resolution: 3.35→60.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 0 0 1137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221160
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9231578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4695148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1725.19252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.88915186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.051155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02884
X-RAY DIFFRACTIONr_nbd_refined0.2680.2542
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.212
X-RAY DIFFRACTIONr_mcbond_it0.6241.5744
X-RAY DIFFRACTIONr_mcangle_it0.78421185
X-RAY DIFFRACTIONr_scbond_it1.1773470
X-RAY DIFFRACTIONr_scangle_it1.9144.5393
LS refinement shellResolution: 3.351→3.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 31 -
Rwork0.269 205 -
obs-31 100 %
Refinement TLS params.Method: refined / Origin x: 5.888 Å / Origin y: 36.729 Å / Origin z: -3.791 Å
111213212223313233
T-0.1863 Å20.075 Å2-0.0317 Å2--0.1187 Å2-0.0119 Å2---0.1103 Å2
L1.1549 °21.852 °2-1.088 °2-4.7404 °2-2.8078 °2--2.4384 °2
S-0.0168 Å °0.0771 Å °-0.0967 Å °-0.0099 Å °-0.1375 Å °-0.2171 Å °0.1507 Å °0.0924 Å °0.1543 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 4017 - 40
2X-RAY DIFFRACTION1AA41 - 10841 - 108
3X-RAY DIFFRACTION1AA109 - 165109 - 165

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