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- PDB-4hep: Complex of lactococcal phage TP901-1 with a llama vHH (vHH17) bin... -

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Basic information

Entry
Database: PDB / ID: 4hep
TitleComplex of lactococcal phage TP901-1 with a llama vHH (vHH17) binder (nanobody)
Components
  • BPP
  • vHH17 domain
KeywordsVIRAL PROTEIN / Alpha-beta / phage receptor binding protein / llama glama vHH domain / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


virus tail, baseplate / cell adhesion / 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 / 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 ...Helix Hairpins - #2190 / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Phage tail base-plate Siphoviridae RBP, head 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesLactococcus phage TP901-1 (virus)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDesmyter, A. / Spinelli, S. / Farenc, C. / Blangy, S. / Bebeacua, C. / van Sinderen, D. / Mahony, J. / Cambillau, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Viral infection modulation and neutralization by camelid nanobodies
Authors: Desmyter, A. / Farenc, C. / Mahony, J. / Spinelli, S. / Bebeacua, C. / Blangy, S. / Veesler, D. / van Sinderen, D. / Cambillau, C.
History
DepositionOct 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BPP
G: vHH17 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2883
Polymers31,1922
Non-polymers961
Water5,855325
1
A: BPP
G: vHH17 domain
hetero molecules

A: BPP
G: vHH17 domain
hetero molecules

A: BPP
G: vHH17 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8639
Polymers93,5756
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area19590 Å2
ΔGint-119 kcal/mol
Surface area34300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.380, 74.380, 375.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein BPP / Baseplate protein


Mass: 17165.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: bpp, ORF49 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9G096
#2: Antibody vHH17 domain


Mass: 14026.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.6M ammonium sulfate, 0.1M MES, 6mg/ml protein complex, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.931 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2012
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.75→48 Å / Num. all: 41184 / Num. obs: 41184 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 36.54 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 33
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2999 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F0C

3f0c


Resolution: 1.75→25.62 Å / Cor.coef. Fo:Fc: 0.9559 / Cor.coef. Fo:Fc free: 0.9587 / Occupancy max: 1 / Occupancy min: 0.33 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.088 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1659 4.03 %RANDOM
Rwork0.1975 ---
all0.1977 41168 --
obs0.1977 41168 99.96 %-
Displacement parametersBiso max: 121.75 Å2 / Biso mean: 42.02 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.1857 Å20 Å20 Å2
2--0.1857 Å20 Å2
3----0.3714 Å2
Refine analyzeLuzzati coordinate error obs: 0.235 Å
Refinement stepCycle: LAST / Resolution: 1.75→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 5 325 2501
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092219HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.133007HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0732SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes045HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0332HARMONIC5
X-RAY DIFFRACTIONt_it02219HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion17.87
X-RAY DIFFRACTIONt_chiral_improper_torsion0287SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact02695SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2213 110 3.69 %
Rwork0.2268 2873 -
all0.2266 2983 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.15620.07110.00560.3889-0.09250.087-0.00340.0055-0.0029-0.00420.0050.0012-0.0018-0.0043-0.00160.0442-0.0124-0.01950.0050.0409-0.0476-0.2384-34.1141-53.2267
20.43150.00440.34990.77540.19740.28340.0030.00080.00360.0006-0.0067-0.02030.0010.00290.00370.02580.0065-0.00070.02280.0042-0.06662.3045-40.3695-30.0423
30.0222-0.0040.1175-0.012-0.07770.3188-0.00120.03170.0459-0.0087-0.0152-0.0154-0.010.01170.01650.0413-0.017-0.0632-0.026-0.0129-0.01182.9861-32.63663.3469
40.2774-0.1065-0.07640.8449-0.14090.3463-0.01140.02410.062-0.0082-0.0012-0.0126-0.02-0.0210.01260.01850.0099-0.0697-0.0331-0.02380.0089-2.7911-28.742713.3016
50.45260.1901-0.46630.2816-0.21330.37130.0055-0.0016-0.00370.0037-0.0250.0134-0.013-0.01560.0195-0.00530.01-0.0464-0.0092-0.01880.0114-4.0642-34.998619.739
60.2203-0.24930.10150.78730.0770.0679-0.0014-0.00530.03380.0061-0.00070.0005-0.00990.00010.00210.0031-0.0007-0.0657-0.0078-0.03710.0022-1.6123-33.435719.0247
7-0.0126-0.08390.03970.3285-0.03510-0.00090.0040.01510.00050.0131-0.0107-0.0055-0.0093-0.0122-0.03120.01640.00760.00640.05080.0291-7.7695-12.1281-36.0594
80.18280.17920.19610.4505-0.28460.2533-0.0064-0.00630.01430.01190.01140.0010.00050.0012-0.0051-0.0586-0.0137-0.03260.01260.00140.05214.4389-18.9992-32.8149
90.2351-0.37090.29860.8578-0.25520.3688-0.00360.00360.00760.0053-0.0003-0.00190.00580.00110.0038-0.0334-0.02180.03110.01360.0850.03050.6423-24.264-38.6946
100.3497-0.1238-0.1855-0.1219-0.02730.16060.00160.00670.0059-0.0032-0.0031-0.0102-0.0054-0.00580.0015-0.032-0.00090.01040.02310.03280.01780.7947-15.6364-41.879
110.3183-0.25390.09860.75170.19540.1203-0.00040.0120.007-0.00940.0111-0.00990.0007-0.0131-0.0108-0.07120.0097-0.01710.03150.06290.0283-7.499-19.4564-38.4096
120.3888-0.01710.0411-0.0435-0.05360.0231-0.0041-0.00060.0112-0.00140.0056-0.00960.00080.0004-0.0015-0.0028-0.00010.01830.0270.0332-0.02057.1935-30.8362-37.6732
130.1090.1451-0.28170.5146-0.00050.2136-0.00760.0020.01240.01170.0223-0.0050.0112-0.0043-0.0147-0.04380.0155-0.03490.0260.00160.0164-5.5721-20.3207-30.9355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - A|17}A2 - 17
2X-RAY DIFFRACTION2{A|18 - A|53}A18 - 53
3X-RAY DIFFRACTION3{A|54 - A|78}A54 - 78
4X-RAY DIFFRACTION4{A|79 - A|116}A79 - 116
5X-RAY DIFFRACTION5{A|117 - A|143}A117 - 143
6X-RAY DIFFRACTION6{A|144 - A|163}A144 - 163
7X-RAY DIFFRACTION7{G|2 - G|20}G2 - 20
8X-RAY DIFFRACTION8{G|21 - G|40}G21 - 40
9X-RAY DIFFRACTION9{G|41 - G|60}G41 - 60
10X-RAY DIFFRACTION10{G|61 - G|80}G61 - 80
11X-RAY DIFFRACTION11{G|81 - G|100}G81 - 100
12X-RAY DIFFRACTION12{G|101 - G|115}G101 - 115
13X-RAY DIFFRACTION13{G|116 - G|131}G116 - 131

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