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- PDB-4avz: Tailspike protein mutant E372Q of E. coli bacteriophage HK620 -

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Basic information

Entry
Database: PDB / ID: 4avz
TitleTailspike protein mutant E372Q of E. coli bacteriophage HK620
ComponentsTAIL SPIKE PROTEIN
KeywordsVIRAL PROTEIN / ENDO-N-ACETYLGLUCOSAMINIDASE / O-ANTIGEN
Function / homology
Function and homology information


endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / virion attachment to host cell / 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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Tail spike protein
Similarity search - Component
Biological speciesSALMONELLA PHAGE HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsGohlke, U. / Broeker, N.K. / Mueller, J.J. / Uetrecht, C. / Heinemann, U. / Seckler, R. / Barbirz, S.
Citation
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. / Muller, J.J. / Uetrecht, C. / Heinemann, U. / Seckler, R. / Barbirz, S.
#1: Journal: Mol.Microbiol. / Year: 2008
Title: Crystal Structure of Escherichia Coli Phage Hk620 Tailspike: Podoviral Tailspike Endoglycosidase Modules are Evolutionarily Related.
Authors: Barbirz, S. / Muller, J.J. / Uetrecht, C. / Clark, A.J. / Heinemann, U. / Seckler, R.
History
DepositionMay 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)64,8272
Polymers64,7041
Non-polymers1221
Water6,071337
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)194,4806
Polymers194,1133
Non-polymers3663
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area21350 Å2
ΔGint-77.9 kcal/mol
Surface area50340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.271, 74.271, 174.665
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

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Components

#1: Protein TAIL SPIKE PROTEIN


Mass: 64704.371 Da / Num. of mol.: 1 / Fragment: RESIDUES 111-710 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA PHAGE HK620 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9AYY6
#2: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 373 TO GLN

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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: 2.17 Å3/Da / Density % sol: 43.38 % / Description: R MEAS HAS BEEN REPORTED AS R MERGE.
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLISED FROM 3.5 M SODIUMFORMATE, 0.1 M TRIS-HCL, PH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 29, 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: 1.82→50 Å / Num. obs: 50917 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 1.82→1.93 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VJI

2vji


Resolution: 1.82→36.128 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.822 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 2546 5 %RANDOM
Rwork0.1672 ---
obs0.169 50915 99.734 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.923 Å20.462 Å20 Å2
2--0.923 Å20 Å2
3----1.385 Å2
Refinement stepCycle: LAST / Resolution: 1.82→36.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 0 8 337 4884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.024739
X-RAY DIFFRACTIONr_bond_other_d0.0020.023006
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9146474
X-RAY DIFFRACTIONr_angle_other_deg1.00637305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44424.435230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77515672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6141523
X-RAY DIFFRACTIONr_chiral_restr0.1180.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025567
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021036
X-RAY DIFFRACTIONr_nbd_refined0.2420.21226
X-RAY DIFFRACTIONr_nbd_other0.1860.275
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22361
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8790.9224739
X-RAY DIFFRACTIONr_mcbond_other0.1930.9353006
X-RAY DIFFRACTIONr_mcangle_it1.3411.376474
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3442.7621542
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6974.9213964
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 174 -
Rwork0.197 3215 -
obs--98.26 %
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)
11.84620.4340.48094.34071.26311.527-0.06040.2224-0.1188-0.418-0.02730.0369-0.0620.09930.08770.12590.00620.01350.11480.01330.02545.615245.1647-10.6296
20.19870.0036-0.03120.074-0.05051.0657-0.06510.0525-0.0569-0.0613-0.0494-0.0260.21930.04950.11440.10040.02590.05350.0529-0.00710.05962.495824.207926.583
31.91720.15760.06470.4723-0.01040.8288-0.0176-0.0117-0.2136-0.0134-0.028-0.0350.17350.02830.04560.0850.0050.01850.0552-0.00490.08540.615823.752954.6445
40.02810.026-0.01350.05380.06420.3764-0.0054-0.0253-0.00840.0227-0.01890.00690.0729-0.0120.02430.03410.00030.00690.04780.00440.0808-2.927929.623379.7635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A112 - 145
2X-RAY DIFFRACTION2A146 - 467
3X-RAY DIFFRACTION3A468 - 532
4X-RAY DIFFRACTION4A533 - 709

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