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- PDB-6gvp: TAILSPIKE PROTEIN MUTANT E372Q (DELTA N471/S472) OF E. COLI BACTE... -

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Basic information

Entry
Database: PDB / ID: 6gvp
TitleTAILSPIKE PROTEIN MUTANT E372Q (DELTA N471/S472) OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH HEXASACCHARIDE
ComponentsTail spike protein
KeywordsVIRAL PROTEIN / 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
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #250 / Hk620 tailspike protein, N-terminal domain-like / Phage spike trimer 2 / Phage spike trimer / 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 ...Elongation Factor Tu (Ef-tu); domain 3 - #250 / Hk620 tailspike protein, N-terminal domain-like / Phage spike trimer 2 / Phage spike trimer / 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: 1.71 Å
AuthorsRoske, Y. / Gohlke, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationBA 4046/1-2 Germany
CitationJournal: 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.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionJul 11, 2018ID: 4XQH
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
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 1.2Aug 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 1.3Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _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.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 / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)65,8899
Polymers64,5031
Non-polymers1,3868
Water12,953719
1
A: Tail spike protein
hetero molecules

A: Tail spike protein
hetero molecules

A: Tail spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,66827
Polymers193,5103
Non-polymers4,15824
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area31710 Å2
ΔGint-86 kcal/mol
Surface area48560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.125, 74.125, 175.122
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1790-

HOH

21A-1799-

HOH

31A-1815-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Tail spike protein


Mass: 64503.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage HK620 (virus) / Plasmid: PET11D / Production host: Escherichia coli BL21 (bacteria) / 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)-[alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-6DGlcpa1-4[DGlcpNAcb1-3]DGalpa1-3[DGlcpa1-6]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5][a2211m-1a_1-5]/1-2-3-4-5-4/a3-b1_a6-f1_b3-c1_b4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-D-Galp]{[(3+1)][b-D-GlcpNAc]{}[(4+1)][a-D-Glcp]{[(6+1)][a-L-Rhap]{}}}[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 726 molecules

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


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


Mass: 46.025 Da / Num. of mol.: 3 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS-HCL, 3.5 M SODIUM FORMATE PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.71→43.78 Å / Num. obs: 61232 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 22.24 Å2 / Rrim(I) all: 0.088 / Net I/σ(I): 19.8
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3127 / Rrim(I) all: 0.786 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOR

4xor


Resolution: 1.71→43.78 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.092 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1741 3057 5 %RANDOM
Rwork0.1363 ---
obs0.1382 58133 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.58 Å2 / Biso mean: 17.137 Å2 / Biso min: 8.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å2-0 Å2
2--0.54 Å2-0 Å2
3----1.74 Å2
Refinement stepCycle: final / Resolution: 1.71→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 0 92 719 5329
Biso mean--19.51 30.31 -
Num. residues----594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024849
X-RAY DIFFRACTIONr_bond_other_d0.0020.024117
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.9346637
X-RAY DIFFRACTIONr_angle_other_deg1.0853.0099575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7555624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30724.348230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58215677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4631524
X-RAY DIFFRACTIONr_chiral_restr0.1180.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025641
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021051
LS refinement shellResolution: 1.71→1.754 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 220 -
Rwork0.221 4213 -
all-4433 -
obs--99.69 %
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)
10.42390.443-0.84843.8456-2.98933.02360.02730.1226-0.0556-0.1733-0.11560.00770.1131-0.08780.08830.09550.00720.00550.0804-0.00190.028732.90421.1036-13.8137
20.0270.0156-0.03620.04650.07060.5923-0.0249-0.0125-0.0128-0.0389-0.04740.0024-0.1592-0.04260.07230.09750.0231-0.02360.04660.00040.028734.145739.220725.6848
30.90380.0704-0.0060.04390.12860.4469-0.0449-0.02390.0116-0.0279-0.00750.0096-0.0947-0.01460.05240.05010.0011-0.01920.0198-0.00350.054436.867839.298455.3557
40.0032-0.00080.0120.0181-0.06070.232-0.0014-0.00940.00540.0123-0.0133-0.0006-0.04870.01350.01480.0408-0.0018-0.00760.044-0.00780.064939.909134.53579.5693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A110 - 134
2X-RAY DIFFRACTION2A0
3X-RAY DIFFRACTION3A0
4X-RAY DIFFRACTION4A0

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