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- PDB-4l97: Structure of the RBP of lactococcal phage 1358 in complex with gl... -

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Basic information

Entry
Database: PDB / ID: 4l97
TitleStructure of the RBP of lactococcal phage 1358 in complex with glucose-1-phosphate
ComponentsReceptor Binding ProteinReceptor (biochemistry)
KeywordsVIRAL PROTEIN / beta sandwich domain / phage receptor binding protein / Lactococcus lactis pellicle saccharides cell wall
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 / 1-O-phosphono-alpha-D-glucopyranose / Putative phage structural protein
Function and homology information
Biological speciesLactococcus phage 1358 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsFarenc, C. / Spinelli, S. / Bebeacua, C. / Tremblay, D. / Orlov, I. / Blangy, S. / Klaholz, B.P. / Moineau, S. / Cambillau, C.
CitationJournal: To be Published
Title: A Virulent Siphophage CyoEM Structure and Host Recognition and Infection Mechanism
Authors: Farenc, C. / Spinelli, S. / Bebeacua, C. / Tremblay, D. / Orlov, I. / Blangy, S. / Klaholz, B.P. / Moineau, S. / Cambillau, C.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 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: Receptor Binding Protein
B: Receptor Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1724
Polymers86,6522
Non-polymers5202
Water7,386410
1
A: Receptor Binding Protein
hetero molecules

A: Receptor Binding Protein
hetero molecules

A: Receptor Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7586
Polymers129,9783
Non-polymers7803
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 area15420 Å2
ΔGint-67 kcal/mol
Surface area44700 Å2
MethodPISA
2
B: Receptor Binding Protein
hetero molecules

B: Receptor Binding Protein
hetero molecules

B: Receptor Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7586
Polymers129,9783
Non-polymers7803
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15470 Å2
ΔGint-69 kcal/mol
Surface area44620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.550, 165.550, 165.550
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 Receptor Binding Protein / Receptor (biochemistry) / RBP


Mass: 43326.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage 1358 (virus) / Gene: ORF20 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3W0F1
#2: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 4.36 Å3/Da / Density % sol: 71.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mM zinc sulfate heptahydrate, 100 mM MES, pH 6.5, 25% v/v PEG550 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.921 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2013
RadiationMonochromator: lower resolution Si(111) cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. all: 45762 / Num. obs: 45762 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 63.13 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.6
Reflection shellResolution: 2.61→2.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3338 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L9B

4l9b


Resolution: 2.61→47.79 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9071 / SU R Cruickshank DPI: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.209 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 2289 5 %RANDOM
Rwork0.1788 ---
all0.1805 45761 --
obs0.1805 45761 99.2 %-
Displacement parametersBiso mean: 57.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.288 Å
Refinement stepCycle: LAST / Resolution: 2.61→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 32 410 6498
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2088SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes910HARMONIC5
X-RAY DIFFRACTIONt_it6232HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion842SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7091SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6232HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8498HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion17.55
LS refinement shellResolution: 2.61→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2295 163 5.01 %
Rwork0.2046 3089 -
all0.2058 3252 -
obs--99.2 %
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)
10.0731-0.0745-0.291200.08620.04570.0008-0.0095-0.00290.0055-0.0017-0.00060.0009-0.00460.00080.00160.03030.0251-0.0137-0.01660.0026-61.349249.2524-35.9704
20.0625-0.33110.20310.45161.22870.2824-0.0027-0.02980.01410.0160.008-0.01560.00440.0124-0.0053-0.00610.0211-0.0233-0.0102-0.02770.0031-39.522334.6233-21.0407
30-0.3737-0.13210.06140.2730.1324-0.0011-0.01340.00940.01350.0043-0.00440.00260.0069-0.003200.01560.0004-0.0006-0.0311-0.0002-41.865837.3461-16.4024
40.0511-0.7806-1.060300.08681.56930.0012-0.01630.02010.0098-0.00670.0090.0187-0.00180.00560.02740.05750.0506-0.0324-0.0409-0.0191-50.826636.6898-13.8581
50-0.3582-0.54190.22110.42360.0767-0.0039-0.00210.00280.00410.00340.01520.0053-0.01080.00050.0150.00140.0452-0.0137-0.0044-0.0053-51.796125.4183-25.9605
60.2725-0.0604-0.12520.15630.27590.022-0.0013-0.0133-0.00390.00920.00560.00230.01180.0138-0.00420.02160.0305-0.01480.00480.0026-0.0345-39.304723.1173-17.3007
70.14630.256-0.31270.04220.01350.35080.0066-0.01180.0034-0.0019-0.00550.00310.01250.0186-0.0010.00420.0361-0.0055-0.04560.00990.0118-26.447619.7086-41.8515
80.0563-0.30390.61130.10190.04050.47480.00460.0015-0.00410.01060.0007-0.00320.01620.0162-0.00530.00340.0529-0.0312-0.03480.0220.0047-21.334615.6056-37.9201
90.1752-0.18530.13880.2827-0.01190.08620.00020.0282-0.00580.00190.00730.00080.0040.0188-0.00750.01050.03620.0024-0.02750.0067-0.0035-26.801813.603-47.6452
100-0.34610.46180.6190.27350.20790.00420.0343-0.0408-0.00350.0033-0.00560.03060.0292-0.00750.00260.02380.0183-0.0299-0.0194-0.0331-32.495310.3011-52.5367
110.00920.0018-0.29610.64630.08340.10280.00090.0209-0.00520.01060.0010.00040.01050.021-0.00190.0060.02790.0128-0.01590-0.0116-28.862716.3361-51.7303
120.1220.07480.10490.1225-0.12770.1069-0.00060.0024-0.00270.00090.0018-0.00050.0024-0.0011-0.00120.01060.02560.0088-0.0175-0.0224-0.0009-22.71311.9318-56.7283
130.0004-0.16150.101300.1287000.0005-0.0012-0.00110.0001-0.00540.00350.00090-0.00230.04460.0023-0.0115-0.00490.0035-12.36162.4412-52.4122
1400.1561-0.23010.46960.149200.00060.00060.0070.0023-0.0035-0.00020.0157-0.00340.0029-0.01640.00760.0147-0.02790.00870.0133-32.180121.4832-47.6417
150.00380.01380.03440.0030.00420.01430.00020.0007-0.00060.00090.00110.0039-0.0008-0.0024-0.00130.0049-0.0056-0.00680.00170.0024-0.0069-48.187620.4231-53.0682
160.01140.32380.19970.10520.04120.00070.00130.00330.0057-0.00090.0022-0.0004-0.0044-0.0029-0.0035-0.0018-0.0199-0.0288-0.0019-0.02850.000226.753713.594712.9455
170.0290.13640.79710.09421.21590.6155-0.0017-0.01570.0150.0003-0.00530.0049-0.0079-0.01920.0070.0197-0.0122-0.0207-0.0063-0.0302-0.02161.740527.18462.8344
1800.07570.24370.1170.25290.0715-0.0005-0.00710.0073-0.0001-0.00010.0057-0.0086-0.00760.00060.0027-0.0083-0.0064-0.0007-0.030603.87531.73145.8574
1900.70750.94811.61680.121300.0013-0.01060.0096-0.01150.004-0.0081-0.00710.0004-0.00520.0217-0.0642-0.0607-0.033-0.0581-0.015312.339435.49444.5412
2000.34040.38580.17390.11930.1777-0.0024-0.0038-0.0045-0.0050.0034-0.0094-0.00540.0183-0.00110.0297-0.058-0.006-0.031-0.0135-0.003113.277424.9744-8.2466
210.17140.4410.21970.22170.22240.06-0.0010.00030.0102-0.0091-0.00940.0074-0.0089-0.0080.01040.02370.0065-0.0297-0.0388-0.01440.006-0.327332.1739-7.997
2200.28860.10910.5213-0.111800.0037-0.02430.0056-0.0061-0.007-0.0005-0.01410.02380.00330.02180.00040.0058-0.0208-0.0009-0.0154-10.66896.7467-13.0906
2300.30140.36640.24560.13360.05370.00380.00230.0083-0.0048-0.0036-0.0038-0.02470.0022-0.00020.03640.00110.0222-0.0477-0.0083-0.003-16.666810.4841-16.0964
240.29670.1822-0.39220.04960.2240.31030.00150.00020.0035-0.002-0.0095-0.003-0.02030.00620.00790.0086-0.0029-0.0011-0.02060.0141-0.0141-10.44891.7527-19.8879
250.1365-0.608-0.33680.4795-0.23160.29860.00730.0288-0.0242-0.0165-0.01620.0107-0.04520.01740.0089-0.0142-0.04860.0157-0.06840.01290.0033-4.6652-1.9615-24.3744
260.2568-0.40340.42610.0878-0.09780.0490.00350.003-0.0035-0.01270.0017-0.0048-0.01850.0051-0.0052-0.0034-0.02410.0058-0.03130.00880.0056-7.6117-2.2775-17.9045
270.0210.11-0.21220.006-0.04840.1260.0005-0.0005-0.0047-0.003-0.00060.0033-0.00150.00250.00010.0046-0.00290.0015-0.00190.0001-0.0122-14.9416-6.4348-32.053
280-0.1335-0.16780.0596-0.07630.00270.00080.0027-0.0003-0.00270.00020.0015-0.0014-0.0044-0.00090.01770.0328-0.0108-0.0290.02880.002-25.5788-3.5024-29.8548
290-0.14890.1660.14330.18870.06990.0014-0.00340.00010.00650.0031-0.0083-0.02560.0032-0.0045-0.0129-0.0064-0.0025-0.00250.0157-0.0058-4.14651.5908-12.7074
300.0002-0.0107-0.02060.0146-0.005300.00010.0006-0.00020.0004-0.0002-0.0025-0.00080.00110.0001-0.0034-0.00350.0048-0.00410.0040.007412.0823-1.6572-16.2091
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

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