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- PDB-4yel: Tailspike protein double mutant D339A/E372A of E. coli bacterioph... -

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Basic information

Entry
Database: PDB / ID: 4yel
TitleTailspike protein double mutant D339A/E372A of E. coli bacteriophage HK620 in complex with hexasaccharide
ComponentsTail spike protein
KeywordsMETAL BINDING 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 / 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 speciesEnterobacteria phage HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGohlke, U. / Broeker, N.K. / Heinemann, U. / Seckler, R. / Barbirz, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationBA 4046/1-1 Germany
Citation
Journal: to be published
Title: Enthalpic cost of water removal from a hydrophobic glucose binding cavity on HK620 tailspike protein.
Authors: Gohlke, U. / Broeker, N.K. / Kunstmann, S. / Santer, M. / Heinemann, U. / Lipowski, R. / Seckler, R. / 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. / Mueller, J.J. / Uetrecht, C. / Heinemann, U. / Seckler, R. / Barbirz, S.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / 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.occupancy / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 3.1Jan 10, 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)65,62611
Polymers64,1481
Non-polymers1,47810
Water13,745763
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)196,87833
Polymers192,4443
Non-polymers4,43530
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 area34000 Å2
ΔGint-64 kcal/mol
Surface area47370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.360, 74.360, 174.679
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-1817-

HOH

21A-1855-

HOH

31A-1862-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Tail spike protein


Mass: 64147.895 Da / Num. of mol.: 1 / Fragment: head binding, RESIDUES 115-710 / Mutation: D339A, E372A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria 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, 772 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.: 763 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 3.5 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 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: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.72→43.67 Å / Num. obs: 60326 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.041 / Net I/σ(I): 17.9 / Num. measured all: 364165
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.72-1.755.80.7632.31759530590.7290.34597.6
9.1-43.674.90.01861.5236248410.00998.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.29data scaling
PHASERphasing
ARPmodel building
Cootmodel building
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AVZ

4avz


Resolution: 1.72→43.67 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1432 / WRfactor Rwork: 0.1121 / FOM work R set: 0.8872 / SU B: 4.195 / SU ML: 0.069 / SU R Cruickshank DPI: 0.0937 / SU Rfree: 0.0931 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1712 3016 5 %RANDOM
Rwork0.135 57309 --
obs0.1368 60326 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.49 Å2 / Biso mean: 16.164 Å2 / Biso min: 7.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å2-0 Å2
2--0.32 Å20 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.72→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4516 0 113 763 5392
Biso mean--17.99 28.76 -
Num. residues----596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194892
X-RAY DIFFRACTIONr_bond_other_d0.0010.024339
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9386699
X-RAY DIFFRACTIONr_angle_other_deg1.07839926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2615633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97924.273227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18115677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9321524
X-RAY DIFFRACTIONr_chiral_restr0.1820.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025866
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021253
X-RAY DIFFRACTIONr_mcbond_it0.6550.9462479
X-RAY DIFFRACTIONr_mcbond_other0.6560.9472480
X-RAY DIFFRACTIONr_mcangle_it0.9721.4183129
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 219 -
Rwork0.221 4163 -
all-4382 -
obs--99.25 %
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)
11.82992.0797-0.84758.2724-2.95052.3219-0.14860.4170.0397-0.55740.0656-0.05330.1164-0.09440.0830.18210.0023-0.01390.1856-0.01090.016831.688518.4199-10.06
20.3363-0.1151-0.01620.94450.48641.8735-0.04430.08920.0601-0.0732-0.0423-0.0011-0.1626-0.03260.08660.10030.0076-0.03670.07570.02790.027533.596340.853910.4724
30.33250.00640.09190.25040.01491.0147-0.030.04350.0641-0.0496-0.02290.027-0.1113-0.00040.05290.02250.0018-0.01430.0080.00560.016235.533239.509839.1877
412.0445-1.0825-0.3534.12940.94373.48250.1562-0.37150.95520.1052-0.0667-0.074-0.72040.2559-0.08940.1747-0.06840.02720.0361-0.03510.077132.197146.648160.3894
51.0149-0.1271-0.08050.1899-0.0420.4618-0.0148-0.07080.08420.045-0.0075-0.0347-0.04970.01450.02220.0142-0.0033-0.00910.0065-0.00340.011439.342537.404969.645
61.2335-0.12240.95970.05720.042.10990.0106-0.0050.01840.0150.0118-0.0209-0.11940.0992-0.02240.04-0.0108-0.0020.0122-0.00670.03841.772730.919193.0369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 142
2X-RAY DIFFRACTION2A143 - 259
3X-RAY DIFFRACTION3A260 - 523
4X-RAY DIFFRACTION4A524 - 536
5X-RAY DIFFRACTION5A537 - 633
6X-RAY DIFFRACTION6A634 - 709

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