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- PDB-2x6y: Tailspike protein mutant D339A of E.coli bacteriophage HK620 in c... -

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Entry
Database: PDB / ID: 2x6y
TitleTailspike protein mutant D339A of E.coli bacteriophage HK620 in complex with hexasaccharide
ComponentsTAIL SPIKE PROTEIN
KeywordsVIRAL PROTEIN / RIGHT-HANDED PARALLEL BETA-HELIX / VIRAL ADHESION PROTEIN / ENDO-N-ACETYLGLUCOSAMINIDASE / HYDROLASE
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
Biological speciesSALMONELLA PHAGE HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLorenzen, N.K. / Mueller, J.J. / Heinemann, U. / Seckler, R. / Barbirz, S.
Citation
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.
#1: Journal: Mol.Microbiol. / Year: 2008
Title: Crystal Structure of Escherichia Coli Phage Hk620 Tailspike: Podoviral Tailspike Endoglycosidase Modules are Evolutionarily Related.
Authors: Barbirz, S. / Muller, J.J. / Uetrecht, C. / Clark, A.J. / Heinemann, U. / Seckler, R.
History
DepositionFeb 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _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.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 / _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_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAIL SPIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8865
Polymers64,6611
Non-polymers1,2254
Water12,484693
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)197,65915
Polymers193,9843
Non-polymers3,67512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area29730 Å2
ΔGint-48.5 kcal/mol
Surface area48500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.336, 74.336, 174.977
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-2152-

HOH

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Components

#1: Protein TAIL SPIKE PROTEIN


Mass: 64661.348 Da / Num. of mol.: 1
Fragment: LACKING THE N-TERMINAL HEAD-BINDING DOMAIN, RESIDUES 111-710
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH HEXASACCHARIDE / 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)-[alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-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]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5][a2122h-1a_1-5][a2211m-1a_1-5]/1-2-1-3-4-3/a3-b1_a6-f1_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]{}}}[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 340 TO ALA
Sequence detailsDELETION 1-110, MUTATION D339A

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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: 2.14 Å3/Da / Density % sol: 42.48 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: VAPOR DIFFUSION, HANGING DROP:PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8,2MM EDTA,0.2M NACL. RERVOIR: 100MM TRIS PH8.5,3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICRO LITER, 0.3 MICRO ...Details: VAPOR DIFFUSION, HANGING DROP:PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8,2MM EDTA,0.2M NACL. RERVOIR: 100MM TRIS PH8.5,3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICRO LITER, 0.3 MICRO LITER 33MM HEXASACCHARIDE. TEMPERATURE 20 DEGREE CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: RAYONIX / Detector: CCD / Date: Oct 2, 2009 / Details: GLAS MIRROR
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.35→37.17 Å / Num. obs: 112857 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.8
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / % possible all: 58.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0108refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VJI

2vji


Resolution: 1.35→43.22 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.923 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.17074 5961 5 %RANDOM
Rwork0.13211 ---
obs0.13406 112857 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.35→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 82 693 5304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224865
X-RAY DIFFRACTIONr_bond_other_d0.0010.023114
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9396638
X-RAY DIFFRACTIONr_angle_other_deg0.8853.0087554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68124.31232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99615702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7671525
X-RAY DIFFRACTIONr_chiral_restr0.0840.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021023
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_it1.43723010
X-RAY DIFFRACTIONr_mcbond_other0.48221245
X-RAY DIFFRACTIONr_mcangle_it2.07734887
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2364.51855
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.34261751
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.14537979
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.353→1.388 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 322 -
Rwork0.234 5834 -
obs--68.81 %

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