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- PDB-4xr6: Tailspike protein double mutant D339A/E372Q of E. coli bacterioph... -

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Basic information

Entry
Database: PDB / ID: 4xr6
TitleTailspike protein double mutant D339A/E372Q of E. coli bacteriophage HK620 in complex with hexasaccharide
ComponentsTail spike protein
KeywordsVIRAL PROTEIN / beta helix / protein-carbohydrate complex / pectin lyase fold / METAL BINDING PROTEIN
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: 1.78 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
DepositionJan 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_audit_support ...diffrn_radiation_wavelength / pdbx_audit_support / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _pdbx_audit_support.funding_organization
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 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)65,76510
Polymers64,3331
Non-polymers1,4329
Water11,692649
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)197,29630
Polymers192,9993
Non-polymers4,29727
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 area33530 Å2
ΔGint-70 kcal/mol
Surface area47600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.404, 74.404, 174.180
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-1719-

HOH

21A-1744-

HOH

31A-1749-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y+1,x-y,z and -x+y+1,-x+1,z.

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Tail spike protein


Mass: 64333.074 Da / Num. of mol.: 1 / Fragment: head binding, UNP residues 114-710 / Mutation: D339A, E372Q
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, 657 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.: 4 / 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.: 649 / 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: 43.14 %
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: 1.78→43.54 Å / Num. obs: 50824 / % possible obs: 93.2 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.028 / Net I/σ(I): 19 / Num. measured all: 257500
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
1.78-1.823.70.3393.8817122250.8680.18671.8
9.08-43.544.90.02139.7241249410.0198.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.29data scaling
REFMACphasing
ARPmodel building
Cootmodel building
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XM3

4xm3


Resolution: 1.78→43.54 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1707 / WRfactor Rwork: 0.1271 / FOM work R set: 0.8787 / SU B: 4.901 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1146 / SU Rfree: 0.1142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 2532 5 %RANDOM
Rwork0.1387 48257 --
obs0.141 48257 93.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.79 Å2 / Biso mean: 17.614 Å2 / Biso min: 7.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 1.78→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 110 649 5288
Biso mean--18.23 27.36 -
Num. residues----597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194807
X-RAY DIFFRACTIONr_bond_other_d0.0010.024279
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9386566
X-RAY DIFFRACTIONr_angle_other_deg0.89639774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4185610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69924.336226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48615666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8741523
X-RAY DIFFRACTIONr_chiral_restr0.1170.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
X-RAY DIFFRACTIONr_mcbond_it0.7261.0052423
X-RAY DIFFRACTIONr_mcbond_other0.7271.0062424
X-RAY DIFFRACTIONr_mcangle_it1.0441.5053038
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 150 -
Rwork0.194 2757 -
all-2907 -
obs--73.19 %
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)
11.87032.1801-0.88959.3143-2.62852.341-0.15260.40970.0848-0.96710.08820.00710.1629-0.07080.06440.2778-0.0077-0.02260.279-0.00540.01931.704719.1507-11.9885
20.2487-0.2577-0.06961.10260.48522.0048-0.03220.14820.0757-0.1151-0.0369-0.0046-0.1409-0.01860.06910.14140.0051-0.03470.12980.05080.03233.680340.700210.0647
30.5108-0.02110.1450.2449-0.04421.1078-0.02820.07930.0772-0.0734-0.01830.017-0.12630.00440.04640.04030.0027-0.01380.01360.01020.014135.59539.489639.0469
413.8397-2.3152-3.08184.9146-3.47124.19810.3462-0.23771.22680.4503-0.0644-0.1883-0.54130.1455-0.28180.3042-0.0294-0.0580.0071-0.0170.143233.165847.337260.1455
50.897-0.09850.07470.1599-0.09930.55950.0008-0.06280.09340.0412-0.0184-0.0236-0.05720.02830.01750.0135-0.0082-0.00370.0093-0.00420.010939.461537.448570.0669
61.2107-0.08920.95830.0392-0.03682.30570.014-0.01870.01910.01060.0083-0.0266-0.12980.081-0.02230.0206-0.0073-0.00560.0067-0.00590.022941.579330.629292.9152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 141
2X-RAY DIFFRACTION2A142 - 259
3X-RAY DIFFRACTION3A260 - 523
4X-RAY DIFFRACTION4A524 - 536
5X-RAY DIFFRACTION5A537 - 636
6X-RAY DIFFRACTION6A637 - 709

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