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

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Basic information

Entry
Database: PDB / ID: 4xnf
TitleTailspike protein double mutant D339A/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 / 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 speciesEnterobacteria phage HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 15, 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 / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _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 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_symmetry / _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 / _struct_conn.pdbx_dist_value / _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_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

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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)64,9449
Polymers64,5451
Non-polymers3988
Water9,728540
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)194,83127
Polymers193,6363
Non-polymers1,19524
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 area24540 Å2
ΔGint-143 kcal/mol
Surface area50100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.222, 74.222, 174.337
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-1422-

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 / head binding domain


Mass: 64545.270 Da / Num. of mol.: 1 / Fragment: UNP residues 112-710 / 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: 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.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 42.73 %
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: RAYONIX MX-225 / Detector: CCD / Date: Nov 20, 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: 1.68→43.11 Å / Num. obs: 64123 / % possible obs: 99.6 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Net I/σ(I): 19.9 / Num. measured all: 338047
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
1.68-1.714.60.7072.11387330440.7060.35294.4
9.05-43.114.40.01365.7216149310.00798.6

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Processing

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

4xm3


Resolution: 1.68→43.11 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1692 / WRfactor Rwork: 0.1312 / FOM work R set: 0.8621 / SU B: 4.699 / SU ML: 0.077 / SU R Cruickshank DPI: 0.0949 / SU Rfree: 0.0978 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 3211 5 %RANDOM
Rwork0.1542 60908 --
obs0.1563 64123 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.62 Å2 / Biso mean: 21.294 Å2 / Biso min: 8.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: final / Resolution: 1.68→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 25 540 5109
Biso mean--23.12 30.32 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194765
X-RAY DIFFRACTIONr_bond_other_d0.0010.024250
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9156505
X-RAY DIFFRACTIONr_angle_other_deg0.90539719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2895622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83924.361227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97615672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7181523
X-RAY DIFFRACTIONr_chiral_restr0.1160.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021234
X-RAY DIFFRACTIONr_mcbond_it0.7911.092456
X-RAY DIFFRACTIONr_mcbond_other0.7971.0912457
X-RAY DIFFRACTIONr_mcangle_it1.1441.6333088
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 231 -
Rwork0.251 4246 -
all-4477 -
obs--95.36 %
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)
18.20740.97270.017911.13564.341117.45880.02860.8692-0.1264-0.9207-0.01120.1435-0.0815-0.2435-0.01730.27660.0079-0.02630.26410.04860.204533.257327.7084-19.6275
20.37750.17090.25991.34920.65592.1412-0.1040.15460.0724-0.0907-0.05610.0148-0.3303-0.08150.16010.2280.0229-0.05920.17460.03620.030633.719836.61787.2801
31.64070.3674-0.13490.90640.1321.7142-0.07710.14960.0894-0.1212-0.07990.0252-0.3709-0.04210.1570.15890.0158-0.05730.06980.01570.028435.284940.363227.4824
41.26860.69820.05790.74920.34121.8236-0.03640.03980.1995-0.135-0.08480.1302-0.2959-0.21280.12120.0840.0331-0.0320.0529-0.00180.041133.675138.465843.087
53.42930.8314-0.25350.82270.16861.6354-0.01480.05930.3684-0.051-0.03970.0965-0.2933-0.08330.05460.05370.0145-0.01640.0080.00270.043836.532940.429554.5376
60.14780.0170.11290.1177-0.16480.9153-0.0064-0.04080.04990.0454-0.0246-0.016-0.10150.0350.0310.0198-0.0078-0.00870.0169-0.01260.024640.122134.60779.5912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A111 - 122
2X-RAY DIFFRACTION2A123 - 252
3X-RAY DIFFRACTION3A253 - 366
4X-RAY DIFFRACTION4A367 - 465
5X-RAY DIFFRACTION5A466 - 532
6X-RAY DIFFRACTION6A533 - 709

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