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- PDB-4xkv: Tailspike protein mutant D339N of E. coli bacteriophage HK620 -

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Basic information

Entry
Database: PDB / ID: 4xkv
TitleTailspike protein mutant D339N of E. coli bacteriophage HK620
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 / Hk620 tailspike protein, N-terminal domain-like / Phage spike trimer 2 / Phage spike trimer / HK620, Tail spike protein, C-terminal / 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 / Hk620 tailspike protein, N-terminal domain-like / Phage spike trimer 2 / Phage spike trimer / HK620, Tail spike protein, C-terminal / 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: 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 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / software / 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_struct_conn_angle.ptnr3_auth_seq_id / _software.classification / _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)64,5326
Polymers64,2491
Non-polymers2835
Water4,720262
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)193,59618
Polymers192,7473
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 area23590 Å2
ΔGint-104 kcal/mol
Surface area49060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.917, 73.917, 174.502
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-959-

HOH

21A-1116-

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

#1: Protein Tail spike protein


Mass: 64248.957 Da / Num. of mol.: 1 / Fragment: head binding, UNP residues 1-596 / Mutation: D339N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage HK620 (virus) / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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.: 262 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2014 / 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→43.05 Å / Num. obs: 26540 / % possible obs: 80.1 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.043 / Net I/σ(I): 10.1 / Num. measured all: 92726
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
2.1-2.162.90.2024.2569619940.9360.11675.7
8.91-43.054.50.05418.121904870.990.0394.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.2.17data scaling
REFMACphasing
ARPmodel building
Cootmodel building
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xm3

4xm3


Resolution: 2.1→43.05 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.871 / WRfactor Rfree: 0.2727 / WRfactor Rwork: 0.2182 / FOM work R set: 0.7506 / SU B: 15.096 / SU ML: 0.209 / SU R Cruickshank DPI: 0.4765 / SU Rfree: 0.2845 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.477 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 1354 5.1 %RANDOM
Rwork0.2267 25176 --
obs0.2296 26530 80.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.45 Å2 / Biso mean: 22.591 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.32 Å20 Å2
2--0.63 Å20 Å2
3----2.06 Å2
Refinement stepCycle: final / Resolution: 2.1→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 18 262 4803
Biso mean--26.57 24.55 -
Num. residues----596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194687
X-RAY DIFFRACTIONr_bond_other_d0.0010.024198
X-RAY DIFFRACTIONr_angle_refined_deg0.9981.9176390
X-RAY DIFFRACTIONr_angle_other_deg0.69939592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63924.241224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43915666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7981524
X-RAY DIFFRACTIONr_chiral_restr0.0610.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021207
X-RAY DIFFRACTIONr_mcbond_it0.2141.4082409
X-RAY DIFFRACTIONr_mcbond_other0.2141.4092410
X-RAY DIFFRACTIONr_mcangle_it0.3742.113017
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 100 -
Rwork0.267 1705 -
all-1805 -
obs--76 %
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)
14.02160.474-0.47717.1535-4.35152.6583-0.10470.45880.2692-0.71280.22370.17130.4504-0.171-0.1190.25810.0072-0.00920.19750.00180.030332.769721.755-12.2268
20.3171-0.070.15421.07210.15210.6052-0.06790.05870.0735-0.0628-0.0612-0.0133-0.1888-0.07230.12910.1269-0.0013-0.04460.11020.02210.042533.571438.14778.501
30.84950.1328-0.02380.7885-0.14420.8286-0.00630.07720.0944-0.0465-0.06540.0072-0.16740.0230.07170.10030.0141-0.03010.09390.01250.037534.753540.080428.5708
40.38740.10290.21150.67320.1620.9451-0.0215-0.07140.107-0.0613-0.02740.0738-0.0726-0.02620.04890.0835-0.0017-0.01020.0678-0.00020.0734.22237.961343.8707
51.56510.24850.25690.69960.22250.58420.0293-0.01370.1756-0.0178-0.05020.0292-0.1287-0.06790.02090.10560.0188-0.00220.08680.00690.08236.447339.562554.3083
64.7722-0.8487-0.68375.03460.05331.9840.0006-0.13430.40430.073-0.02590.0189-0.19570.12130.02520.0752-0.0018-0.0210.1174-0.01740.055630.680642.457860.8243
70.0959-0.03880.02920.2064-0.17120.227-0.0182-0.02710.02090.0212-0.0217-0.0063-0.07150.01430.03990.06380.003-0.00960.0638-0.00450.082339.95836.638373.5075
80.5191-0.06870.13810.22080.37771.13110.0407-0.0090.03340.0342-0.0234-0.022-0.03650.0897-0.01720.0738-0.02360.00150.09610.00160.078741.084730.44591.4262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 132
2X-RAY DIFFRACTION2A133 - 252
3X-RAY DIFFRACTION3A253 - 378
4X-RAY DIFFRACTION4A379 - 466
5X-RAY DIFFRACTION5A467 - 527
6X-RAY DIFFRACTION6A528 - 540
7X-RAY DIFFRACTION7A541 - 645
8X-RAY DIFFRACTION8A646 - 709

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