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- PDB-4xlh: Tailspike protein double mutant D339A/E372A of E. coli bacterioph... -

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Basic information

Entry
Database: PDB / ID: 4xlh
TitleTailspike protein double mutant D339A/E372A 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: 1.91 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_struct_conn_angle / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8638
Polymers64,4881
Non-polymers3757
Water8,089449
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)194,59024
Polymers193,4653
Non-polymers1,12621
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 area24040 Å2
ΔGint-106 kcal/mol
Surface area50220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.975, 73.975, 174.328
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-1341-

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: 64488.223 Da / Num. of mol.: 1 / Fragment: head binding, residues 112-710 / Mutation: D339A, E372A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK620 (virus) / Plasmid: pET11d / Production host: Escherichia coli BL21(DE3) (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.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 42.39 %
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 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: 1.91→43.04 Å / Num. obs: 43960 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.051 / Net I/σ(I): 14.1 / Num. measured all: 237608
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
1.91-1.955.10.7612.11404627520.6520.36894
8.94-43.044.50.02149.4226150710.01198.1

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Processing

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

4xm3


Resolution: 1.91→43.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1767 / WRfactor Rwork: 0.1269 / FOM work R set: 0.8435 / SU B: 8.075 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1488 / SU Rfree: 0.1426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 2189 5 %RANDOM
Rwork0.1574 41623 --
obs0.1601 43960 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.13 Å2 / Biso mean: 23.005 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å2-0 Å2
3----1.69 Å2
Refinement stepCycle: final / Resolution: 1.91→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 24 449 5013
Biso mean--29.69 29.68 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194722
X-RAY DIFFRACTIONr_bond_other_d0.0010.024218
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9166438
X-RAY DIFFRACTIONr_angle_other_deg0.85339640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2355612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44124.311225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25915665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8341523
X-RAY DIFFRACTIONr_chiral_restr0.1040.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
X-RAY DIFFRACTIONr_mcbond_it0.871.3262431
X-RAY DIFFRACTIONr_mcbond_other0.8761.3272432
X-RAY DIFFRACTIONr_mcangle_it1.2851.9873048
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 160 -
Rwork0.261 3028 -
all-3188 -
obs--99.87 %
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)
13.00782.4523-1.1069.1921-3.11912.5535-0.21520.48850.1304-0.77030.09560.03740.2581-0.19430.11960.17570.0222-0.01420.2283-0.01430.02731.432219.4174-10.7859
20.27250.04350.14840.1990.02342.2168-0.08180.09770.0927-0.109-0.05650.0481-0.3484-0.07180.13830.11840.0234-0.05140.06960.01360.051434.479440.062326.2975
32.56090.3881-0.11410.97110.21480.9319-0.0342-0.00020.1859-0.0323-0.02130.016-0.2362-0.05330.05540.06270.0134-0.01990.0031-0.00340.018836.360939.309253.7311
416.42533.2248-2.97448.944-2.36926.61880.1919-0.37031.24790.2729-0.10280.0876-0.99890.0509-0.08910.15930.0061-0.00950.0238-0.03410.102131.895946.672460.2569
50.16030.00210.16350.0473-0.18050.9847-0.0059-0.07170.03130.0373-0.0249-0.0149-0.12450.04190.03090.0421-0.0081-0.0130.0499-0.01410.069940.382134.307980.0685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A111 - 146
2X-RAY DIFFRACTION2A147 - 464
3X-RAY DIFFRACTION3A465 - 524
4X-RAY DIFFRACTION4A525 - 537
5X-RAY DIFFRACTION5A538 - 709

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