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- PDB-4rga: Phage 1358 receptor binding protein in complex with the trisaccha... -

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Basic information

Entry
Database: PDB / ID: 4rga
TitlePhage 1358 receptor binding protein in complex with the trisaccharide GlcNAc-Galf-GlcOMe
ComponentsPhage 1358 receptor binding protein (ORF20)
KeywordsVIRAL PROTEIN / alpha/beta protein / phage receptor binding protein / Lactococcus lactis SMQ388
Function / homologyViral head domain of polysaccharide receptor-binding protein-like / Triple-stranded beta-helix / Phage fibre proteins / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Putative phage structural protein
Function and homology information
Biological speciesLactococcus phage 1358 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSpinelli, S. / Mccabe, O. / Farenc, C. / Tremblay, D. / Blangy, S. / Oscarson, S. / Moineau, S. / Cambillau, C.
CitationJournal: Mol.Microbiol. / Year: 2015
Title: The targeted recognition of Lactococcus lactis phages to their polysaccharide receptors.
Authors: McCabe, O. / Spinelli, S. / Farenc, C. / Labbe, M. / Tremblay, D. / Blangy, S. / Oscarson, S. / Moineau, S. / Cambillau, C.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage 1358 receptor binding protein (ORF20)
B: Phage 1358 receptor binding protein (ORF20)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8034
Polymers86,6842
Non-polymers1,1192
Water15,151841
1
A: Phage 1358 receptor binding protein (ORF20)
hetero molecules

A: Phage 1358 receptor binding protein (ORF20)
hetero molecules

A: Phage 1358 receptor binding protein (ORF20)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7056
Polymers130,0263
Non-polymers1,6793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area14530 Å2
ΔGint-70 kcal/mol
Surface area44450 Å2
MethodPISA
2
B: Phage 1358 receptor binding protein (ORF20)
hetero molecules

B: Phage 1358 receptor binding protein (ORF20)
hetero molecules

B: Phage 1358 receptor binding protein (ORF20)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7056
Polymers130,0263
Non-polymers1,6793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area14520 Å2
ΔGint-74 kcal/mol
Surface area44360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.370, 166.370, 166.370
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 Phage 1358 receptor binding protein (ORF20)


Mass: 43342.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage 1358 (virus) / Gene: ORF20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3W0F1
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-galactofuranose-(1-6)-methyl alpha-D-glucopyranoside


Type: oligosaccharide / Mass: 559.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DGalfb1-6DGlcp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_1*OC][a2112h-1b_1-4][a2122h-1b_1-5_2*NCC/3=O]/1-2-3/a6-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Glcp]{[(6+1)][b-D-Galf]{[(2+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / 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: 4.43 Å3/Da / Density % sol: 72.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 13 mg/ml in a solution containing 10 mM Zinc Sulfate Heptahydrate, 100 mM MES buffer pH 6.5., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Nov 10, 2013
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: 2.1→48 Å / Num. all: 89232 / Num. obs: 89232 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 39.67 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7218 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L92

4l92


Resolution: 2.1→48 Å / Cor.coef. Fo:Fc: 0.9484 / Cor.coef. Fo:Fc free: 0.9483 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 4462 5 %RANDOM
Rwork0.1805 ---
all0.1811 ---
obs0.1811 89232 100 %-
Displacement parametersBiso mean: 47.57 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.237 Å
Refinement stepCycle: LAST / Resolution: 2.1→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 76 841 6973
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016292HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.128586HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d02128SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0174HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0918HARMONIC5
X-RAY DIFFRACTIONt_it06292HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.98
X-RAY DIFFRACTIONt_other_torsion17.03
X-RAY DIFFRACTIONt_chiral_improper_torsion0864SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact07667SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2063 327 5 %
Rwork0.1878 6213 -
all0.1887 6540 -
obs--100 %
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)
10.09920.07010.429200.05920.1850.0010.00890.00170.00040-0.00080.0039-0.0064-0.00110.0055-0.0382-0.03720.0007-0.02660.0007-61.1618-48.3413-46.9941
20.11090.37380.15060.55370.97750.23770.00040.0096-0.016-0.00180.0054-0.01790.0059-0.0021-0.0058-0.0046-0.00880.0162-0.025-0.0470.0151-38.1815-35.2655-61.5309
30-0.001-0.20120.11760.28920.0324-0.00210.0192-0.0024-0.0070-0.004-0.00310.00770.00210.00460.0044-0.0097-0.0177-0.06610.0164-40.4645-38.0496-66.1527
40.02151.37361.52990-0.18171.30810.0040.0302-0.0202-0.0166-0.01290.0071-0.0164-0.01150.00890.0203-0.0515-0.0867-0.0168-0.0862-0.0368-49.2565-36.9533-69.0379
500.58170.4660.2650.28510.2255-0.00370.0117-0.0118-0.0152-0.00020.0195-0.0097-0.00490.00390.02850.0052-0.0754-0.00910.0052-0.0183-50.2391-25.3123-57.4599
60.02730.1520.0880-0.16860.10190.00040.01250.0012-0.02260.00640.0076-0.0120.0125-0.00680.0275-0.02480.03270.0126-0.0304-0.0389-37.4414-24.0521-65.6572
70.6737-0.2047-0.17830.215-0.18210.12540.00960.01050.00630.0032-0.0176-0.0118-0.0350.02350.0079-0.0011-0.0488-0.0078-0.07130.020.0446-25.3003-20.1026-40.8666
80.3073-0.2069-0.37710.1525-0.24490.11560.0040.00230.0168-0.0154-0.0094-0.0295-0.02480.03780.00540.0043-0.04640.0513-0.04380.04080.0339-19.8622-16.3954-44.7007
90.0084-0.04150.29580.61170.38010.15060.0062-0.02060.0233-0.0010.0062-0.0545-0.0265-0.0019-0.01230.0293-0.05230.0253-0.03990.02670.0005-25.6555-13.7799-35.3066
100.3320.20170.39720.77760.45580.17530.0172-0.01320.0629-0.00120-0.0142-0.0620.0059-0.01730.0425-0.02020.0169-0.0286-0.005-0.0307-31.5153-9.9839-30.833
110.0402-0.0460.40220.42720.31620.07230.0044-0.01760.01760.01450.0101-0.0369-0.01810.0105-0.01450.0168-0.0461-0.0013-0.0182-0.0002-0.0099-27.9953-16.2035-31.2409
120.0383-0.13020.02340.1949-0.28240.2235-0.0001-0.00880.00310.00180.0012-0.0006-0.00320.0038-0.00110.0184-0.0481-0.0171-0.0254-0.03610.0116-21.3701-1.9451-26.5751
130.01310.3576-0.10180.03730.288900.00110.00090.00060.0002-0.003-0.0042-0.00110.00170.0019-0.0056-0.0687-0.0137-0.0209-0.00840.0272-10.9026-3.0593-30.3831
140.0589-0.5417-0.050.77810.15440.25750.0019-0.00510.0004-0.00140.006-0.0181-0.0211-0.0143-0.0079-0.0225-0.0332-0.0198-0.02940.02530.0205-31.3715-21.4052-35.2367
150.0012-0.0236-0.072300.05710.03630.0002-0.0007-0.0002-0.00250.00080.0042-0.0009-0.0031-0.0010.0080.00680.02680.0064-0.0033-0.0113-47.508-19.4811-30.5164
160.0536-0.3186-0.17270.12390.097700.0011-0.0012-0.0089-0.00290.0007-0.0040.0014-0.0011-0.00180.00320.03140.04270.002-0.0227-0.001327.6577-14.0235-97.3693
170.1138-0.0779-1.03550.09061.15230.21790.00020.0127-0.0046-0.0047-0.0020.00170.0025-0.02620.00180.0050.04540.0310.0044-0.0561-0.01793.5224-28.1134-86.0844
180-0.0592-0.29730.02050.42490-0.00090.0049-0.0087-0.00040.00440.0050.009-0.0108-0.00350.00280.04250.0170.0045-0.0478-0.01045.7385-32.6895-88.9859
190.0419-1.1873-1.59041.497-0.04240.00340.00080.026-0.01510.01090.0133-0.00510.0110.0075-0.01410.01940.1050.0798-0.0411-0.0947-0.015714.3512-36.0252-87.6039
200.025-0.5688-0.88860.27360.40420.1231-0.00390.01-0.00260.01140.0031-0.00530.00880.01310.00090.03290.11640.0256-0.0465-0.02170.003215.2472-25.0777-75.3967
210.0138-0.3384-0.71870.24310.13700.0021-0.0027-0.00870.0072-0.00780.00790.0137-0.0120.00570.02820.02870.0393-0.0391-0.04760.01052.0557-32.7122-75.1319
220.2857-0.4173-0.30870.64110.20010.04710.00870.0274-0.01770.0164-0.0109-0.01230.01630.02090.00230.04890.00540.0024-0.0224-0.0234-0.0318-9.1338-7.5859-70.5483
230.1220.0102-0.63680.2908-0.14190.20450.00730.0015-0.01530.0051-0.0070.00620.0530.0007-0.00040.0644-0.00350.0186-0.0462-0.006-0.018-14.9749-11.3426-67.267
240.4688-0.0627-0.20860.49880.12370.18420.00550.00390.00110.0036-0.0092-0.00820.0391-0.00340.00370.03580.03240.0093-0.03720.0082-0.0184-8.9189-2.3251-63.9152
250.23940.3042-0.1490.38230.30390.75240.0114-0.02490.01950.0369-0.01730.01120.07170.05230.0060.00580.0507-0.0157-0.0696-0.02290.0126-3.03571.6884-59.6913
260.25930.2839-0.22240.26440.37810.5074-0.0010.0144-0.0014-0.00070.0047-0.01610.0420.0194-0.00370.01850.04390.0169-0.04130.00850.0025-6.23871.691-66.083
270-0.36720.36610.1495-0.25050.22750.001-0.0060.00360.01-0.0032-0.0002-0.00380.00350.00220.02310.02170.0076-0.0075-0.022-0.0126-13.3086.1121-51.9771
280.00040.09370.09120.11910.02490.02160.0018-0.00030.00460.00190.0007-0.0018-0.0004-0.0048-0.00250.0375-0.03280.0355-0.03370.0348-0.006-23.85942.8253-53.7336
290.00010.0828-0.06930.42510.22170.06060.0040.00710.00280.0045-0.0098-0.02850.02790.00720.0058-0.0010.05510.01150.0020.0174-0.0107-2.789-2.222-71.2927
300.02090.04280.01610.0401-0.045200-0.0008-0.0004-0.0004-0.0003-0.0015-0.00110.0020.0003-0.01160.0076-0.0065-0.00290.00540.01713.42311.5978-68.3689
310-0.0597-0.02010-0.02690.02750.0005-0.00130.0010.0002-0.00140.00120.00190.00070.0010.00720.01280.0018-0.0014-0.0026-0.0028-4.4914-8.6045-53.3823
3200.00340.0330.01840.011200.0002-0.00050.0006-0.00080.00010.0018-0.00070.0007-0.00020.006-0.0043-0.0015-0.0055-0.00580.0032-30.8042-3.0345-41.1754
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|170 }A144 - 170
7X-RAY DIFFRACTION7{ A|171 - A|206 }A171 - 206
8X-RAY DIFFRACTION8{ A|207 - A|236 }A207 - 236
9X-RAY DIFFRACTION9{ A|237 - A|269 }A237 - 269
10X-RAY DIFFRACTION10{ A|270 - A|319 }A270 - 319
11X-RAY DIFFRACTION11{ A|320 - A|343 }A320 - 343
12X-RAY DIFFRACTION12{ A|344 - A|355 }A344 - 355
13X-RAY DIFFRACTION13{ A|356 - A|366 }A356 - 366
14X-RAY DIFFRACTION14{ A|367 - A|387 }A367 - 387
15X-RAY DIFFRACTION15{ A|388 - A|393 }A388 - 393
16X-RAY DIFFRACTION16{ B|2 - B|17 }B2 - 17
17X-RAY DIFFRACTION17{ B|18 - B|53 }B18 - 53
18X-RAY DIFFRACTION18{ B|54 - B|78 }B54 - 78
19X-RAY DIFFRACTION19{ B|79 - B|116 }B79 - 116
20X-RAY DIFFRACTION20{ B|117 - B|143 }B117 - 143
21X-RAY DIFFRACTION21{ B|144 - B|170 }B144 - 170
22X-RAY DIFFRACTION22{ B|171 - B|206 }B171 - 206
23X-RAY DIFFRACTION23{ B|207 - B|236 }B207 - 236
24X-RAY DIFFRACTION24{ B|237 - B|269 }B237 - 269
25X-RAY DIFFRACTION25{ B|270 - B|319 }B270 - 319
26X-RAY DIFFRACTION26{ B|320 - B|343 }B320 - 343
27X-RAY DIFFRACTION27{ B|344 - B|355 }B344 - 355
28X-RAY DIFFRACTION28{ B|356 - B|366 }B356 - 366
29X-RAY DIFFRACTION29{ B|367 - B|387 }B367 - 387
30X-RAY DIFFRACTION30{ B|388 - B|393 }B388 - 393
31X-RAY DIFFRACTION31{ B|401 - B|401 }B401
32X-RAY DIFFRACTION32{ A|401 - A|401 }A401

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