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- PDB-4l92: Structure of the RBP from lactococcal phage 1358 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4l92
TitleStructure of the RBP from lactococcal phage 1358 in complex with 2 GlcNAc molecules
ComponentsReceptor Binding ProteinReceptor (biochemistry)
KeywordsVIRAL PROTEIN / beta sandwich domain / phage receptor binding protein / Lactococcus lactis pellicle saccharide
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 / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Putative phage structural protein
Function and homology information
Biological speciesLactococcus phage 1358 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Receptor Binding Protein
B: Receptor Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,70811
Polymers86,6522
Non-polymers1,0569
Water14,988832
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)131,89418
Polymers129,9783
Non-polymers1,91615
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 area17360 Å2
ΔGint-248 kcal/mol
Surface area44090 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)131,23015
Polymers129,9783
Non-polymers1,25212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16380 Å2
ΔGint-269 kcal/mol
Surface area43900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.640, 165.640, 165.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-403-

ZN

21B-402-

ZN

31B-822-

HOH

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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: pERG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3W0F1
#2: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 4.37 Å3/Da / Density % sol: 71.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.921 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 88185 / Num. obs: 88185 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 42.07 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 10 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.3 / Num. unique all: 14123 / % possible all: 99.7

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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: 2.1→30.75 Å / Cor.coef. Fo:Fc: 0.9543 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.114 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 4404 5 %RANDOM
Rwork0.1764 ---
all0.1772 88079 --
obs0.1772 88079 100 %-
Displacement parametersBiso mean: 49.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 0 51 832 6941
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2113SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes178HARMONIC2
X-RAY DIFFRACTIONt_gen_planes917HARMONIC5
X-RAY DIFFRACTIONt_it6266HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion849SEMIHARMONIC5
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_contact7583SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6266HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8543HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion16.75
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2022 325 5.01 %
Rwork0.2044 6161 -
all0.2043 6486 -
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)
10.0208-0.036-0.28230-0.01390.09240.0007-0.0061-0.0015-0.00030.001-0.0007-0.003-0.0034-0.00170.00260.02720.0283-0.0053-0.0144-0.0001-61.165148.669-36.0399
20.0981-0.3407-0.01840.50810.90110.1485-0.0005-0.00760.01040.00110.0058-0.0126-0.00320.0008-0.0054-0.00370.0158-0.0195-0.0146-0.04110.0038-38.723534.9567-21.2572
30-0.15820.19670.07550.18430-0.001-0.0130.00220.0052-0.0009-0.00240.00040.00590.00190.00030.00240.0093-0.0092-0.0470.0111-41.025537.717-16.667
40.0162-0.9637-1.25490-0.19521.12180.0025-0.01490.01450.0112-0.0090.00530.0089-0.00440.00650.01450.05470.0663-0.0077-0.0676-0.0244-49.871736.8532-13.9256
50.0278-0.5063-0.41580.22890.36110.1247-0.0031-0.00820.00520.0084-0.00050.00970.0073-0.00370.00360.01640.0030.0576-0.0107-0.0001-0.0031-50.845625.302-25.7309
60.044-0.2271-0.19750-0.11110.15850.0004-0.0109-0.00040.01290.00280.00160.00660.0089-0.00320.01970.0301-0.00560.0044-0.0079-0.0217-38.107623.561-17.2831
70.64680.13970.07990.0937-0.00990.30080.0052-0.0055-0.0014-0.007-0.0079-0.00550.02630.01630.0026-0.00750.06580.0148-0.04770.00640.0305-25.73519.9256-41.9686
80.21190.00670.380.1439-0.42430.26290.0035-0.0014-0.010.0096-0.0008-0.01960.01510.0264-0.00270.01480.0727-0.0361-0.04150.0330.0236-20.421316.0721-38.0936
90.08590.0785-0.31550.62360.09950.13990.00240.0197-0.0170.0010.0117-0.03330.0130.003-0.01420.02210.0533-0.012-0.03230.00670.0036-26.080213.7116-47.6257
100.3437-0.198-0.34250.54080.31270.26150.01030.0182-0.04110.00390.0025-0.01380.03760.0085-0.01280.03260.02090.0048-0.0192-0.0133-0.0267-31.781510.1459-52.2825
110.0237-0.0721-0.18240.4860.11710.0290.00190.0071-0.0073-0.01150.004-0.01790.0130.0025-0.00590.01630.0441-0.001-0.01620.0003-0.0027-28.29616.2295-51.6786
120.09040.1971-0.01370.1735-0.13620.125-0.00060.0046-0.0009-0.00380.0016-0.00060.0044-0.0003-0.0010.01450.03660.0227-0.0194-0.030.0098-22.29342.2526-56.3325
130.0125-0.25110.05540.00470.249100.0006-0.0018-0.00080.0007-0.001-0.00210.00140.00090.0004-0.00260.05130.0174-0.0135-0.01440.0185-11.45022.8166-52.4229
140.08720.4584-0.07030.7504-0.12630.14510.00010.00480.0002-0.00280.0025-0.00840.0123-0.0022-0.0026-0.01310.04250.0223-0.02720.00730.0187-31.653121.4373-47.6557
150.00140.00850.039500.00530.03950.00030.0005-0.00020.0011-0.00020.00260.0015-0.0016-0.00010.0030.0017-0.01760.0073-0.0018-0.0074-47.732119.8732-52.6808
160.04210.2570.120.13290.053300.00040.00140.0060.00160.0002-0.0021-0.0002-0.0006-0.00070.0019-0.0199-0.03460.0017-0.0155-0.001227.253413.833913.6736
170.04940.14131.01490.05460.83680.02490.0014-0.00540.00630.00220.00060.0004-0.0041-0.0235-0.00210.0028-0.0329-0.02610.0014-0.0386-0.00972.786427.78282.7987
1800.0560.36560.00070.31950-0.0001-0.00340.00650.00180.00340.0046-0.0051-0.0063-0.00340.0041-0.0277-0.0170.004-0.0339-0.01054.846732.52756.0528
190.01151.13051.01411.2-0.208600.002-0.01140.0124-0.01110.0062-0.0064-0.00980.0025-0.00810.0194-0.0828-0.0576-0.0299-0.0667-0.008113.575835.85024.4678
200.00130.4150.6450.19760.35270.1352-0.003-0.00380.0026-0.00760.0014-0.00220.00080.00910.00160.0249-0.0928-0.0281-0.0262-0.03050.001114.43524.9699-7.9995
210.01220.27060.61790.24370.374400.00160.00390.0069-0.0031-0.00280.0033-0.0068-0.00920.00120.0198-0.0212-0.0356-0.0254-0.03240.00371.015632.5042-8.1686
220.19950.33890.33970.51110.05360.00360.0055-0.01740.0066-0.0182-0.00620.0017-0.00990.02080.00080.0361-0.0207-0.0158-0.0242-0.0269-0.0186-9.82197.2061-12.7822
230.1095-0.17040.96720.6594-0.09290.31030.0055-0.00680.0081-0.0044-0.00010.0059-0.03920.0087-0.00540.04590.0076-0.0299-0.0406-0.0007-0.0075-15.719110.9481-15.9544
240.39540.07670.26880.25460.11760.3610.00240.0017-0.0069-0.0039-0.0136-0.0039-0.02510.0010.01130.028-0.018-0.0119-0.03090.0115-0.0096-9.15112.4359-19.2809
250.1846-0.17490.16150.21270.07560.67580.00930.0238-0.0147-0.0253-0.01410.0135-0.05830.04550.0048-0.0032-0.06070.0076-0.0517-0.00570.0077-3.7607-1.7478-23.7163
260.2883-0.32830.34250.15730.13920.71210-0.00330.00550.0031-0.0055-0.0152-0.03780.01950.00540.0137-0.022-0.0055-0.01740.0089-0.0127-6.8306-1.941-17.4012
270.0180.0761-0.16130.1449-0.17790.16830.00030.0034-0.0014-0.0069-0.00040.00040.0028-0.00080.00010.0117-0.0098-0.0107-0.0034-0.0149-0.0045-13.6816-5.6063-31.0035
280-0.1353-0.01750.0216-0.01040.07020.00090.0001-0.001-0.00340.0004-0.00220.0003-0.0049-0.00130.02390.0233-0.0311-0.0150.0301-0.009-24.6068-3.1181-29.5482
2900.08330.11510.48540.17290.09640.0023-0.0067-0.00090.0032-0.0064-0.0036-0.02310.00990.0041-0.0076-0.0457-0.01120.00310.0051-0.0011-3.38261.947-12.1765
300.0172-0.0145-0.00810.0132-0.030500.00010.0007-0.00020.00110.0001-0.00170.00030.0012-0.0001-0.0061-0.0090.0069-0.00030.0030.00912.818-1.6406-15.34
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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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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