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- PDB-4rgg: Structure of the lactococcal phage 1358 receptor binding protein ... -

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Basic information

Entry
Database: PDB / ID: 4rgg
TitleStructure of the lactococcal phage 1358 receptor binding protein in complex with GlcNAc-1P
ComponentsPutative phage structural protein
KeywordsVIRAL PROTEIN / Alpha/beta protein / phage receptor bonding protein (anti-receptor) / L. lactis SMQ-388 surface polysaccharides (pellicle)
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 / Chem-GN1 / Putative phage structural protein
Function and homology information
Biological speciesLactococcus phage 1358 (virus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.15 Å
AuthorsSpinelli, S. / Moineau, S. / Cambillau, C.
CitationJournal: To be Published
Title: Structure of the 1358 lactococcal phage RBP in complex with GlcNAc-1P
Authors: Spinelli, S. / Moineau, S. / Cambillau, C.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 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 / 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.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 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative phage structural protein
B: Putative phage structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2864
Polymers86,6842
Non-polymers6022
Water9,044502
1
A: Putative phage structural protein
hetero molecules

A: Putative phage structural protein
hetero molecules

A: Putative phage structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9306
Polymers130,0263
Non-polymers9043
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area15830 Å2
ΔGint-63 kcal/mol
Surface area44020 Å2
MethodPISA
2
B: Putative phage structural protein
hetero molecules

B: Putative phage structural protein
hetero molecules

B: Putative phage structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9306
Polymers130,0263
Non-polymers9043
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15920 Å2
ΔGint-64 kcal/mol
Surface area43850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.910, 165.910, 165.910
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-577-

HOH

21A-736-

HOH

31B-552-

HOH

41B-661-

HOH

51B-715-

HOH

61B-723-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 2 - 393 / Label seq-ID: 2 - 393

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative phage structural protein


Mass: 43342.027 Da / Num. of mol.: 2 / Fragment: UNP residues 2-393
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: Sugar ChemComp-GN1 / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE / N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE / N-acetyl-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 4.39 Å3/Da / Density % sol: 71.98 %
Crystal growTemperature: 293 K / pH: 6.2
Details: 20% w/v polyethyleneglycol 1000, 100 mM sodium/potassium phosphate buffer, pH 6.2, 200 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2014
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→48 Å / Num. obs: 81936 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.5
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.43 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 4L92

4l92


Resolution: 2.15→47.89 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.136 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3914 4.7 %RANDOM
Rwork0.18 ---
obs0.181 78636 100 %-
all-38297 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.25 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.322 Å
Refinement stepCycle: LAST / Resolution: 2.15→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 38 502 6596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0196228
X-RAY DIFFRACTIONr_bond_other_d0.0050.025667
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.9448495
X-RAY DIFFRACTIONr_angle_other_deg1.093312967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217280
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021530
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4443.3673116
X-RAY DIFFRACTIONr_mcbond_other3.4443.3673115
X-RAY DIFFRACTIONr_mcangle_it5.1095.0263888
X-RAY DIFFRACTIONr_mcangle_other5.4584.4483889
X-RAY DIFFRACTIONr_scbond_it4.3753.7193108
X-RAY DIFFRACTIONr_scbond_other4.3133.2973109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.744.8234606
X-RAY DIFFRACTIONr_long_range_B_refined9.31830.1245361
X-RAY DIFFRACTIONr_long_range_B_other9.34130.1455188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 22783 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 279 -
Rwork0.301 5750 -
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)
11.17191.0363-0.76291.4169-1.37221.4708-0.0544-0.0542-0.19820.2103-0.0681-0.176-0.31740.06930.12240.1650.0041-0.02510.0730.0120.077-26.253-45.94639.116
21.0176-0.2599-0.28060.8157-0.6350.7708-0.00430.116-0.00330.0752-0.2256-0.2585-0.02710.21240.22990.11210.0671-0.09770.21740.03190.1521-13.752-46.22636.097
30.5183-0.32270.6170.26-0.41781.2213-0.02930.1750.04790.0874-0.0766-0.03730.03080.23070.10590.10860.0283-0.00310.11140.01090.0661-24.292-43.36425.829
40.432-0.21290.01910.3170.04550.3799-0.00280.07720.02390.00190.0509-0.0387-0.12380.0645-0.04820.0915-0.02740.01440.09310.02620.0513-40.844-22.03514.478
50.2569-0.25430.10790.4118-0.12950.4241-0.01470.0839-0.0092-0.05490.03580.0464-0.0263-0.0213-0.0210.0768-0.023-0.00590.14210.03950.0499-51.559-26.71811.749
60.2536-0.32920.18110.6267-0.27710.4787-0.00780.0941-0.0399-0.0490.02040.0974-0.0137-0.0179-0.01250.0656-0.0227-0.01560.15590.02170.0505-51.91-31.44813.317
70.275-0.24040.02140.8735-0.25430.4837-0.01070.0828-0.00350.0042-0.00090.0356-0.043-0.03070.01150.07240.00060.00230.07390.04160.0455-50.91-28.05714.726
81.11091.3001-0.40412.0107-1.09430.9816-0.02220.0252-0.34110.2003-0.0019-0.3566-0.24780.00640.02410.1252-0.0138-0.01320.0978-0.04670.19135.99310.78223.178
91.02841.05820.12391.15970.40141.20650.21-0.1728-0.11660.2178-0.2073-0.1444-0.0181-0.2491-0.00270.1321-0.0524-0.08090.1991-0.05120.11173.88210.00935.828
101.00350.65060.62530.43260.38280.44160.0865-0.1645-0.04510.0744-0.0845-0.04410.0066-0.1378-0.0020.0877-0.025-0.01520.1537-0.05610.0379-6.9257.12925.844
110.29440.0961-0.12690.34470.10850.2495-0.011-0.1359-0.02520.01880.0021-0.030.0053-0.02170.00890.06220.0028-0.00480.15940.00830.0304-18.003-13.8758.534
120.20810.11870.06030.29560.08680.374-0.018-0.07280.0239-0.0654-0.01660.0258-0.027-0.08040.03460.0661-0.00260.00020.1037-0.01780.0254-21.73-8.667-1.569
130.29970.12920.23790.40570.13930.2565-0.0268-0.08170.0447-0.0728-0.0040.0106-0.0474-0.07660.03090.07660.00480.00120.0827-0.01650.0432-20.561-3.822-1.656
140.40150.1902-0.13520.60560.17910.254-0.0168-0.0748-0.0183-0.04690.019-0.0561-0.0403-0.0432-0.00220.07830.0078-0.01080.1196-0.01060.0248-18.842-7.184-1.03
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 61
2X-RAY DIFFRACTION2A62 - 121
3X-RAY DIFFRACTION3A122 - 181
4X-RAY DIFFRACTION4A182 - 241
5X-RAY DIFFRACTION5A242 - 301
6X-RAY DIFFRACTION6A302 - 351
7X-RAY DIFFRACTION7A352 - 393
8X-RAY DIFFRACTION8B2 - 61
9X-RAY DIFFRACTION9B62 - 121
10X-RAY DIFFRACTION10B122 - 181
11X-RAY DIFFRACTION11B182 - 241
12X-RAY DIFFRACTION12B242 - 301
13X-RAY DIFFRACTION13B302 - 351
14X-RAY DIFFRACTION14B352 - 393

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