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- PDB-4xl9: Tailspike protein mutant D339A of E. coli bacteriophage HK620 -

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Basic information

Entry
Database: PDB / ID: 4xl9
TitleTailspike protein mutant D339A 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 / 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: 2.02 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 13, 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
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.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 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)64,5254
Polymers64,3341
Non-polymers1913
Water7,945441
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)193,57612
Polymers193,0023
Non-polymers5739
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 area22150 Å2
ΔGint-104 kcal/mol
Surface area49240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.495, 73.495, 174.472
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-1303-

HOH

21A-1331-

HOH

31A-1333-

HOH

41A-1336-

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: 64334.059 Da / Num. of mol.: 1 / Fragment: UNP residues 114-710 / Mutation: D339A
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.: 1 / 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.: 441 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 3.5 M Sodiumformiate

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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: Oct 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: 2.02→42.93 Å / Num. obs: 35142 / % possible obs: 95.8 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.056 / Net I/σ(I): 8 / Num. measured all: 136596
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
2.02-2.072.40.3072495820440.8510.20276.3
9.03-42.934.80.03717.623214860.9990.01798.7

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Processing

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

4xm3


Resolution: 2.02→42.93 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2322 / WRfactor Rwork: 0.1722 / FOM work R set: 0.7755 / SU B: 12.36 / SU ML: 0.166 / SU R Cruickshank DPI: 0.2394 / SU Rfree: 0.1966 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / 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
Rfree0.2432 1751 5 %RANDOM
Rwork0.1873 33327 --
obs0.1901 35142 95.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.02 Å2 / Biso mean: 26.399 Å2 / Biso min: 11.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å20 Å2
3----2.23 Å2
Refinement stepCycle: final / Resolution: 2.02→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 12 441 4982
Biso mean--26.06 32.43 -
Num. residues----597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194665
X-RAY DIFFRACTIONr_bond_other_d0.0010.024182
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9166359
X-RAY DIFFRACTIONr_angle_other_deg0.72239551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76624.286224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44915661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4431523
X-RAY DIFFRACTIONr_chiral_restr0.0690.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025587
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021202
X-RAY DIFFRACTIONr_mcbond_it0.5971.7362398
X-RAY DIFFRACTIONr_mcbond_other0.5971.7372399
X-RAY DIFFRACTIONr_mcangle_it0.9982.6032998
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 100 -
Rwork0.248 1942 -
all-2042 -
obs--76.25 %
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)
11.80461.8768-1.02726.5131-2.38282.5167-0.13010.28080.0763-0.53250.0354-0.00970.1785-0.05480.09470.1467-0.005-0.02060.1561-0.00560.024931.324518.4129-10.5768
20.4803-0.05640.32440.26960.37651.7852-0.0770.09650.0836-0.0718-0.0985-0.0085-0.3596-0.02260.17550.15420.0136-0.05140.08640.05130.060233.848140.22079.8541
30.53870.00670.05370.46-0.02271.3619-0.04990.03410.0973-0.0751-0.05260.0442-0.1968-0.03360.10250.09740.0059-0.03980.04630.01530.074933.596338.809233.8488
41.4260.3372-0.2960.46920.06141.23030.01680.07480.1651-0.0378-0.01590.0557-0.14890.0082-0.0010.09280.0116-0.01110.06060.02120.115536.569240.170454.9898
50.03830.02970.06230.1612-0.09850.4547-0.0103-0.01410.02710.0201-0.0058-0.0299-0.06190.03530.01610.0377-0.00510.00030.0539-0.00270.128640.258934.151380.7041
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 141
2X-RAY DIFFRACTION2A142 - 252
3X-RAY DIFFRACTION3A253 - 453
4X-RAY DIFFRACTION4A454 - 542
5X-RAY DIFFRACTION5A543 - 709

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