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- PDB-4xon: Tailspike protein double mutant D339N/E372Q of E. coli bacterioph... -

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Basic information

Entry
Database: PDB / ID: 4xon
TitleTailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620
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 / 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 / molecular replacement / Resolution: 2.1 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 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 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_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 / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)64,8726
Polymers64,5881
Non-polymers2835
Water4,342241
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)194,61518
Polymers193,7653
Non-polymers85015
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 area23230 Å2
ΔGint-106 kcal/mol
Surface area50630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.172, 74.172, 174.611
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
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

#1: Protein Tail spike protein


Mass: 64588.293 Da / Num. of mol.: 1 / Fragment: head binding, UNP residues 112-710 / Mutation: D339N, E372Q
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: 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
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 42.7 %
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 8, 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: 2.1→43.65 Å / Num. obs: 33244 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.047 / Net I/σ(I): 14.5 / Num. measured all: 190913
Reflection shell

Diffraction-ID: 1 / Redundancy: 5 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.1-2.160.6022.51308325930.8140.29197.5
8.91-43.650.01949.9255951610.00998.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.94 Å43.65 Å
Translation5.94 Å43.65 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.27data scaling
PHASER2.5.2phasing
ARPmodel building
Cootmodel building
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOR

4xor


Resolution: 2.1→43.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1957 / WRfactor Rwork: 0.1362 / FOM work R set: 0.8148 / SU B: 12.731 / SU ML: 0.161 / SU R Cruickshank DPI: 0.2339 / SU Rfree: 0.1971 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1663 5 %RANDOM
Rwork0.1734 31581 --
obs0.1766 33244 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.9 Å2 / Biso mean: 29.597 Å2 / Biso min: 12.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.41 Å20 Å2
2--0.81 Å2-0 Å2
3----2.64 Å2
Refinement stepCycle: final / Resolution: 2.1→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 18 241 4806
Biso mean--32.44 31.44 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194714
X-RAY DIFFRACTIONr_bond_other_d0.0010.024214
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9156427
X-RAY DIFFRACTIONr_angle_other_deg0.8539628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05924.386228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92815667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5081523
X-RAY DIFFRACTIONr_chiral_restr0.1490.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021218
X-RAY DIFFRACTIONr_mcbond_it0.9081.6222421
X-RAY DIFFRACTIONr_mcbond_other0.9081.6232422
X-RAY DIFFRACTIONr_mcangle_it1.3782.4323032
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 117 -
Rwork0.249 2204 -
all-2321 -
obs--96.59 %
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)
10.85121.49480.03994.80410.61390.8688-0.03960.29770.0565-0.364-0.05210.11290.0103-0.09130.09170.30880.0367-0.02010.38740.01410.041933.212525.3477-7.2816
20.89620.1672-0.04360.6353-0.14512.0239-0.07180.21470.1564-0.1655-0.04350.0289-0.4105-0.03620.11530.2520.0124-0.0540.17520.02740.046534.582641.138822.2054
32.0181-0.2239-0.13270.4649-0.03882.76030.03390.30920.1788-0.1287-0.1210.1922-0.3394-0.31140.08710.11880.044-0.070.1131-0.02990.12431.191137.790442.8051
43.35410.5683-0.78240.9190.12271.8896-0.01580.03760.3137-0.0655-0.02830.0237-0.3071-0.03740.0440.05990.0047-0.02910.00240.00580.058337.894140.477354.4253
50.19750.01930.25050.0887-0.20520.9917-0.0068-0.06090.04870.045-0.0441-0.022-0.130.04160.05090.0267-0.0162-0.01090.0416-0.02040.130240.569534.678980.5915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A111 - 165
2X-RAY DIFFRACTION2A166 - 380
3X-RAY DIFFRACTION3A381 - 448
4X-RAY DIFFRACTION4A449 - 542
5X-RAY DIFFRACTION5A543 - 709

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