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- PDB-4l9b: Structure of native RBP from lactococcal phage 1358 (CsI derivative) -

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Basic information

Entry
Database: PDB / ID: 4l9b
TitleStructure of native RBP from lactococcal phage 1358 (CsI derivative)
ComponentsReceptor Binding ProteinReceptor (biochemistry)
KeywordsVIRAL PROTEIN / beta sandwich domain / phage receptor binding protein / Lactococcus lactis pellicle cell wall polyphosphosaccharide
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 / SAD / Resolution: 1.75 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 1.1Jun 13, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_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 / _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: Receptor Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1237
Polymers43,3261
Non-polymers7976
Water6,449358
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)132,37021
Polymers129,9783
Non-polymers2,39218
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area11530 Å2
ΔGint-434 kcal/mol
Surface area43050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.610, 107.610, 107.610
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-405-

CS

21A-406-

CS

31A-782-

HOH

41A-783-

HOH

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Components

#1: Protein Receptor Binding Protein / Receptor (biochemistry) / RBP


Mass: 43326.004 Da / Num. of mol.: 1
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: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 20% w/v PEG1000, 100 mM sodium/potassium phosphate, pH 6.2, 200 mM sodium chloride, 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: 1.55 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2012 / 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: 1.55 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 41979 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 24.3
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
SHELXSphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→25.36 Å / Cor.coef. Fo:Fc: 0.9595 / Cor.coef. Fo:Fc free: 0.9521 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.103 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.099 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 2100 5 %RANDOM
Rwork0.1693 ---
obs0.1708 41979 99.8 %-
all-41979 --
Displacement parametersBiso mean: 42.44 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.181 Å
Refinement stepCycle: LAST / Resolution: 1.75→25.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 6 358 3207
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012917HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13972HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d973SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes427HARMONIC5
X-RAY DIFFRACTIONt_it2917HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.02
X-RAY DIFFRACTIONt_other_torsion15.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion395SEMIHARMONIC5
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_contact3621SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2399 151 5 %
Rwork0.22 2868 -
all0.221 3019 -
obs--99.8 %
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)
10.00150.051-0.01070-0.04030.00690.00010.00020.00040.00030.0002-0.0009-0.00030.0001-0.00030.0012-0.00540.00440.00010.0037-0.0008-12.197233.7561.8518
20.17620.277-0.04250.0892-0.2720.06240.00440.00260.0061-0.0029-0.00550.0091-0.00870.00230.00110.00940.00590.01550.00020.0188-0.0122-23.342725.60640.7876
300.2553-0.10170-0.22270.02590.00120.00180.0023-0.0036-0.00210.006-0.0050.00110.00090.0045-0.01090.01810.00440.0152-0.0087-20.421127.8043-3.3046
40.00610.4872-0.672400.32980.1653-0.00060.0060.0112-0.0019-0.0068-0.0017-0.00110.00370.00740.0008-0.00370.04440.0172-0.0036-0.0172-12.642324.3301-6.2228
50.30440.1952-0.375700.1490.07780.00070.006-0.001-0.0012-0.0069-0.0094-0.0017-0.00190.0062-0.0275-0.0250.0790.0328-0.0286-0.0067-10.941816.77985.5469
60.23390.0884-0.173600.32280.33670.00490.00290.0012-0.0057-0.00490.0098-0.00760.002500.00770.01990.0450.0278-0.019-0.0352-23.500214.2389-2.8718
70.3327-0.15550.15910.1213-0.09470.21590.01240.0299-0.008-0.02-0.0077-0.00790.00780.0044-0.0047-0.0074-0.01280.0192-0.0063-0.03010.0122-36.427510.673721.8364
80.3122-0.3110.21140.13780.12080.32210.00660.0068-0.0169-0.03060.02030.01310.0223-0.005-0.02690.0025-0.03790.01350.0068-0.0308-0.0173-41.21187.275117.581
90.96620.25140.21990.2429-0.22610.24690.0057-0.0079-0.0313-0.02910.0238-0.0130.01920.0063-0.0295-0.0079-0.02380.0278-0.0099-0.04420.001-35.73255.218427.3336
100.17530.22130.31520.4884-0.25850.30410.0101-0.0087-0.0575-0.01560.022-0.03720.0450.0061-0.0321-0.0324-0.01250.02040.0008-0.03060.0194-27.28072.825429.39
110.48740.05790.25750.52820.00420.1310.0013-0.0031-0.0226-0.00510.01980.01320.00780.0121-0.0211-0.0256-0.02090.02420.0139-0.02150.0034-33.82117.708531.4509
120.0103-0.11530.01880.12630.02010.02230.0006-0.0069-0.0068-0.00060.004-0.00220.0044-0.0011-0.0046-0.0061-0.0327-0.0074-0.00750.01750.0195-40.3715-6.827336.3043
130.07580.1611-0.0270.0846-0.22800.00070.0008-0.0064-0.0002-0.00120.00060.00210.00080.0005-0.0036-0.0499-0.0143-0.00980.01420.0211-50.5992-5.801632.1941
140.07560.01120.2130.3221-0.16590.27910.00450.00040.0014-0.01490.0072-0.00710.00440.013-0.0117-0.0144-0.03120.0293-0.0084-0.03040.0192-30.499112.865827.4268
150.0128-0.00810.00730.00790.0394000.0003-0.00060.0001-0.001-0.0007-0.00050.00110.001-0.0069-0.00260.00090.0098-0.00480.0006-14.467111.691732.9471
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

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