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- PDB-6g0x: TAILSPIKE PROTEIN OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 6g0x
TitleTAILSPIKE PROTEIN OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH PENTASACCHARIDE
ComponentsTail spike protein
KeywordsHYDROLASE / BETA HELIX / PROTEIN-CARBOHYDRATE COMPLEX / PECTIN LYASE FOLD
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component / metal ion binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #250 / Phage spike trimer 2 / Phage spike trimer / HK620, Tail spike protein, C-terminal / Hk620 tailspike protein, N-terminal domain-like / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Arc Repressor Mutant, subunit A / Single-stranded right-handed beta-helix, Pectin lyase-like ...Elongation Factor Tu (Ef-tu); domain 3 - #250 / Phage spike trimer 2 / Phage spike trimer / HK620, Tail spike protein, C-terminal / Hk620 tailspike protein, N-terminal domain-like / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Arc Repressor Mutant, subunit A / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Elongation Factor Tu (Ef-tu); domain 3 / Helix non-globular / Special / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Tail spike protein
Similarity search - Component
Biological speciesSalmonella phage HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsGohlke, U. / Broeker, N.K. / Seckler, R. / Barbirz, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationBA 4046/1-2 Germany
Citation
Journal: J. Am. Chem. Soc. / Year: 2018
Title: Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site.
Authors: Kunstmann, S. / Gohlke, U. / Broeker, N.K. / Roske, Y. / Heinemann, U. / Santer, M. / Barbirz, S.
#1: Journal: Glycobiology / Year: 2013
Title: Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity.
Authors: Broeker, N.K. / Gohlke, U. / Muller, J.J. / Uetrecht, C. / Heinemann, U. / Seckler, R. / Barbirz, S.
History
DepositionMar 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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: Tail spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,90611
Polymers64,5901
Non-polymers1,31610
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint3 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.320, 74.320, 174.871
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1849-

HOH

21A-1894-

HOH

31A-1896-

HOH

41A-1898-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Tail spike protein


Mass: 64590.270 Da / Num. of mol.: 1 / Fragment: HEAD BINDING, RESIDUES 112-710
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage HK620 (virus) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9AYY6
#2: Polysaccharide alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-6DGlcpa1-4[DGlcpNAcb1-3]DGalpa1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5][a2122h-1a_1-5][a2211m-1a_1-5]/1-2-1-3-4/a3-b1_b3-c1_b4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-D-Galp]{[(3+1)][b-D-GlcpNAc]{}[(4+1)][a-D-Glcp]{[(6+1)][a-L-Rhap]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 813 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS-HCL, 3.5 M SODIUMFORMIATE / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 6, 2012 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→43.21 Å / Num. obs: 107055 / % possible obs: 98.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XSCALEdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vji

2vji


Resolution: 1.41→43.21 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.407 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.177 5344 5 %RANDOM
Rwork0.147 ---
obs0.149 107054 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.41→43.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 102 804 5453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194941
X-RAY DIFFRACTIONr_bond_other_d0.0010.024370
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.936765
X-RAY DIFFRACTIONr_angle_other_deg0.965310005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4865645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59324.444234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73615690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6521524
X-RAY DIFFRACTIONr_chiral_restr0.1740.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025977
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021269
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_it0.580.6822515
X-RAY DIFFRACTIONr_mcbond_other0.580.6832516
X-RAY DIFFRACTIONr_mcangle_it0.8441.0253181
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.41→1.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 349 -
Rwork0.256 6772 -
obs--89.66 %
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)
12.6199-3.89436.152930.85754.946322.73490.44380.1812-0.1944-1.8021-0.3110.78720.18880.0265-0.13280.4805-0.0482-0.16640.88410.1390.243433.530825.928-24.0757
20.96391.374-0.91759.7724-4.90014.4278-0.05210.18190.0347-0.3821-0.01310.02780.0917-0.15260.06520.10770.0029-0.00990.1413-0.01440.008932.643919.2947-10.0102
30.2252-0.01490.18120.7850.56161.4798-0.05730.07350.0515-0.0733-0.03640.0009-0.1946-0.02430.09370.10150.0152-0.03410.06250.01860.023934.139238.91898.5937
46.1826-4.4016-2.301210.00513.00874.50840.01550.02360.128-0.0382-0.1240.5707-0.3442-0.43260.10850.16270.038-0.03060.2279-0.00250.163818.387242.350422.1255
50.47980.06650.02080.3906-0.01661.167-0.03310.01850.0442-0.0552-0.04710.0184-0.1542-0.02570.08020.04040.0093-0.02210.0079-0.00190.014334.630639.028734.4417
61.34360.2304-0.11120.51710.0940.7533-0.030.01420.1299-0.0201-0.0080.0333-0.135-0.01140.0380.02620.0014-0.01180.00050.00060.015837.948140.407853.344
711.2583-0.7175-2.19165.4129-3.32915.34730.2461-0.17791.05290.2932-0.0656-0.0853-0.76280.1931-0.18050.1458-0.01340.00590.0189-0.0250.106532.610847.949560.4178
80.1429-0.01940.09040.0289-0.10760.4883-0.0165-0.04520.03550.0263-0.007-0.0085-0.0760.02260.02350.0306-0.0046-0.00620.0208-0.00860.026239.961736.610874.7975
92.3022-1.8929-0.25161.65240.45550.8579-0.0705-0.0550.29390.02010.0933-0.2192-0.18360.1915-0.02270.073-0.03470.00450.064-0.01460.05640.467332.903286.7852
100.75010.11680.54280.0663-0.11621.24830.0570.0001-0.04270.0183-0.0028-0.0026-0.00940.0415-0.05420.0252-0.007-0.00580.0302-0.00980.032942.023629.674993.0747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A111 - 115
2X-RAY DIFFRACTION2A116 - 134
3X-RAY DIFFRACTION3A135 - 250
4X-RAY DIFFRACTION4A251 - 259
5X-RAY DIFFRACTION5A260 - 453
6X-RAY DIFFRACTION6A454 - 524
7X-RAY DIFFRACTION7A525 - 536
8X-RAY DIFFRACTION8A537 - 650
9X-RAY DIFFRACTION9A651 - 667
10X-RAY DIFFRACTION10A668 - 709

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