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- PDB-2bse: Structure of Lactococcal Bacteriophage p2 Receptor Binding Protei... -

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Basic information

Entry
Database: PDB / ID: 2bse
TitleStructure of Lactococcal Bacteriophage p2 Receptor Binding Protein in complex with a llama VHH domain
Components
  • LLAMA IMMUNOGLOBULIN
  • RECEPTOR BINDING PROTEIN
KeywordsRECEPTOR / LACTOCOCCUS LACTIS / PHAGE / RECEPTOR BINDING PROTEIN / LLAMA ANTIBODY / VHH
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
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 / Immunoglobulins / Immunoglobulin-like ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor binding protein
Similarity search - Component
Biological speciesLACTOCOCCUS VIRUS P2
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSpinelli, S. / Desmyter, A. / Verrips, C.T. / de Haard, H.J.W. / Moineau, S. / Cambillau, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Lactococcal Bacteriophage P2 Receptor Binding Protein Structure Suggests a Common Ancestor Gene with Bacterial and Mammalian Viruses.
Authors: Spinelli, S. / Desmyter, A. / Verrips, C.T. / de Haard, H.J.W. / Moineau, S. / Cambillau, C.
History
DepositionMay 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 7, 2018Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RECEPTOR BINDING PROTEIN
B: RECEPTOR BINDING PROTEIN
C: RECEPTOR BINDING PROTEIN
D: LLAMA IMMUNOGLOBULIN
E: LLAMA IMMUNOGLOBULIN
F: LLAMA IMMUNOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)126,5046
Polymers126,5046
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.763, 83.939, 137.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RECEPTOR BINDING PROTEIN


Mass: 28668.057 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS VIRUS P2 / Production host: ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: Q71AW2
#2: Antibody LLAMA IMMUNOGLOBULIN


Mass: 13499.944 Da / Num. of mol.: 3 / Fragment: VHH RECOGNITION DOMAIN, RESIDUES 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Cell: LYMPHOCYTE / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. obs: 23055 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.6
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BSD

2bsd


Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.884 / SU B: 16.719 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.192 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1005 4.2 %RANDOM
Rwork0.251 ---
obs0.253 23055 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.72 Å2
Baniso -1Baniso -2Baniso -3
1-4.92 Å20 Å20 Å2
2---6.44 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 0 1 5311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0215436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8831.9237371
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8235681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024203
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1730.22088
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2531.53375
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.47425409
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.46432061
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7994.51962
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.392 71
Rwork0.318 1637
Refinement TLS params.Method: refined / Origin x: 17.333 Å / Origin y: 21.128 Å / Origin z: 27.817 Å
111213212223313233
T0.0501 Å20.0485 Å20.0837 Å2-0.3125 Å2-0.0376 Å2--0.2356 Å2
L1.5985 °20.4126 °2-0.9745 °2-1.3843 °2-0.6201 °2--1.8743 °2
S-0.3645 Å °0.0461 Å °-0.2237 Å °-0.0227 Å °0.1466 Å °-0.0811 Å °0.307 Å °-0.0488 Å °0.2179 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A158 - 264
2X-RAY DIFFRACTION1B158 - 264
3X-RAY DIFFRACTION1C158 - 264
4X-RAY DIFFRACTION1D2 - 123
5X-RAY DIFFRACTION1E2 - 123
6X-RAY DIFFRACTION1F2 - 123

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