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- PDB-2vji: Tailspike protein of E.coli bacteriophage HK620 -

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Basic information

Entry
Database: PDB / ID: 2vji
TitleTailspike protein of E.coli bacteriophage HK620
ComponentsTAILSPIKE PROTEIN
KeywordsVIRAL PROTEIN / VIRAL ADHESION PROTEIN / ENDO-N-ACETYLGLUCOSAMINIDASE / RIGHT-HANDED PARALLEL BETA-HELIX / HYDROLASE / TAILSPIKE
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component
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 / 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 ...Elongation Factor Tu (Ef-tu); domain 3 - #250 / Hk620 tailspike protein, N-terminal domain-like / Phage spike trimer 2 / Phage spike trimer / 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
PHOSPHATE ION / Tail spike protein
Similarity search - Component
Biological speciesBACTERIOPHAGE HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 Å
AuthorsMueller, J.J. / Barbirz, S. / Uetrecht, C. / Seckler, R. / Heinemann, U.
CitationJournal: Mol.Microbiol. / Year: 2008
Title: Crystal Structure of Escherichia Coli Phage Hk620 Tailspike: Podoviral Tailspike Endoglycosidase Modules are Evolutionarily Related.
Authors: Barbirz, S. / Mueller, J.J. / Uetrecht, C. / Clark, A.J. / Heinemann, U. / Seckler, R.
History
DepositionDec 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Advisory / Other / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAILSPIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0185
Polymers64,7051
Non-polymers3134
Water16,844935
1
A: TAILSPIKE PROTEIN
hetero molecules

A: TAILSPIKE PROTEIN
hetero molecules

A: TAILSPIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,05415
Polymers194,1163
Non-polymers93812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area24210 Å2
ΔGint-110.1 kcal/mol
Surface area62150 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.216, 74.216, 175.160
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-2059-

HOH

21A-2130-

HOH

31A-2193-

HOH

41A-2361-

HOH

51A-2481-

HOH

61A-2523-

HOH

71A-2526-

HOH

81A-2528-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TAILSPIKE PROTEIN / HK620 TAILSPIKE PROTEIN


Mass: 64705.355 Da / Num. of mol.: 1
Fragment: LACKING THE N-TERMINAL HEAD-BINDING DOMAIN, RESIDUES 111-710
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE HK620 (virus) / Strain: H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9AYY6

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Non-polymers , 5 types, 939 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE WAS NUMBERED WITHOUT THE N-TERMINAL MET FROM 1 TO 709 (SWISSPROT 1 TO 710)

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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: 2.13 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 3
Details: VAPOR DIFFUSION,HANGING DROP: PROTEIN CONCENTRATION 3MG/ML,5% PEG1500,PH3.0. RESERVOIR: 10% PEG 1500, PH 3.0. DROPLET 3 MICRO LITER: 3 MICRO LITER. CRYO CONDITION:30% PEG1500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 8, 2001 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.38→20 Å / Num. obs: 115675 / % possible obs: 97.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.1 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
SOLVERESOLVE V2.09phasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.38→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.023 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 5722 5 %RANDOM
Rwork0.15 ---
obs0.151 108474 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 17 935 5488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224806
X-RAY DIFFRACTIONr_bond_other_d0.0020.024129
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9196567
X-RAY DIFFRACTIONr_angle_other_deg0.81339572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7675623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5924.217230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.08915700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3241526
X-RAY DIFFRACTIONr_chiral_restr0.0890.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025607
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021044
X-RAY DIFFRACTIONr_nbd_refined0.1910.21005
X-RAY DIFFRACTIONr_nbd_other0.1960.24418
X-RAY DIFFRACTIONr_nbtor_refined0.180.22491
X-RAY DIFFRACTIONr_nbtor_other0.0830.22818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2722
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.2161
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.2149
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.38→1.43 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.237 496 -
Rwork0.208 9521 -
obs--89.37 %
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)
17.82944.9389-1.530210.57181.067223.2109-0.22180.57740.0993-0.82710.3821-0.2027-0.1052-0.1073-0.16030.1624-0.03460.00580.11650.0328-0.0481-33.0643-15.226-18.3785
23.21451.0893-0.46190.72460.3930.91610.00740.03150.014-0.0988-0.04560.0321-0.0869-0.22480.03820.10030.0013-0.01840.13980.0001-0.0343-45.1227-19.1288-4.7306
30.7480.49960.04050.4524-0.58683.177-0.11520.0905-0.0171-0.2126-0.07780.0309-0.0340.41670.1930.1134-0.0490.02020.13130.0523-0.0718-22.6963-11.17995.2281
42.1373-0.02-0.02340.4253-1.01812.4395-0.01730.11120.297-0.1029-0.2296-0.0025-0.44140.30420.24690.1528-0.0805-0.01420.0950.0792-0.0388-22.9331-3.270615.4994
513.51237.55862.97667.29462.13143.1114-0.04890.385-0.1978-0.2573-0.0232-0.12390.0880.51430.0720.0799-0.01040.080.24650.0983-0.0945-14.7459-15.085714.47
67.4964-0.73144.27481.81320.23665.5739-0.11210.45440.2488-0.2621-0.0973-0.0578-0.33050.63910.20940.0577-0.13330.04140.22190.1312-0.0143-10.3983-5.969820.1399
74.1369-0.6415-1.81462.52672.01283.16910.25040.05070.6065-0.341-0.0507-0.1146-0.68370.1787-0.19970.2374-0.05380.00690.04370.07110.0222-26.94193.611421.1326
80.7123-0.1726-0.03430.6595-0.06371.1642-0.02580.10650.0661-0.122-0.0627-0.0688-0.13450.26970.08840.0747-0.03990.00550.1020.05440.0122-21.4182-9.779426.8171
96.8481-9.3779-1.265517.22672.84773.329-0.13270.0213-0.2049-0.09310.03350.4036-0.0417-0.03560.09920.0652-0.0077-0.01360.05440.02760.0248-34.3908-8.988733.9056
100.4758-0.19050.070.4571-0.01540.9384-0.05140.04810.0745-0.0292-0.0223-0.0359-0.13950.13380.07380.048-0.0186-0.00760.04640.03340.0321-24.5529-10.103641.5135
113.31250.5741-0.46267.76230.0881.17240.09510.1924-0.0497-0.1092-0.1139-0.07170.02780.36930.01880.00250.00840.01930.1560.02470.0652-7.8542-19.358249.3135
121.0159-0.40040.07111.01520.14670.8825-0.00650.06490.1552-0.069-0.0284-0.1081-0.10160.10120.03490.0591-0.01440.00740.05880.02790.074-22.2267-10.605953.2857
130.8349-0.3797-0.19431.38190.12510.69040.0025-0.00610.0686-0.0074-0.0197-0.1257-0.01520.09730.01720.058-0.0075-0.00130.06940.01190.089-21.4772-14.517160.4185
140.1783-0.1719-0.11890.79680.06850.3196-0.0008-0.00970.0162-0.0046-0.0084-0.0872-0.01430.09590.00910.0223-0.00190.00020.03520.00740.0953-19.2716-15.94467.2036
154.9631-1.5761.63730.5342-0.44440.7089-0.1880.09440.43920.07760.0303-0.1922-0.19720.1180.15780.0422-0.0387-0.01830.02450.01120.1341-20.9053-1.68470.9798
160.3085-0.0518-0.04060.23120.0590.1456-0.0011-0.02820.02490.01380.0062-0.0838-0.04420.0646-0.0050.02560.00630.00020.0178-0.00070.0824-24.0691-14.794276.3487
173.691.6882-1.5924.3623-3.0673.23240.1034-0.08410.18650.0856-0.02580.20920.00630.0374-0.07760.01150.02370.0020.0306-0.01090.0995-26.6216-22.008102.1506
180.8567-0.43380.91491.0909-0.23211.0384-0.03470.02180.0592-0.0238-0.024-0.1587-0.03150.12220.05870.0080.00910.01580.03580.0030.1126-25.0632-17.395788.3414
191.1357-0.30620.43410.2734-0.58081.29260.0295-0.0691-0.0322-0.0660.05190.07190.11690.0712-0.08150.04720.0168-0.00720.0289-0.00670.1225-28.6363-21.309494.7664
200.4504-0.23280.25850.16620.03510.76860.0241-0.0129-0.0441-0.00750.02470.03570.02980.0327-0.04880.03840.007-0.00240.04730.00270.1184-26.7182-22.057490.507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A112 - 122
2X-RAY DIFFRACTION2A123 - 149
3X-RAY DIFFRACTION3A150 - 202
4X-RAY DIFFRACTION4A203 - 226
5X-RAY DIFFRACTION5A227 - 235
6X-RAY DIFFRACTION6A236 - 243
7X-RAY DIFFRACTION7A244 - 259
8X-RAY DIFFRACTION8A260 - 347
9X-RAY DIFFRACTION9A348 - 353
10X-RAY DIFFRACTION10A354 - 452
11X-RAY DIFFRACTION11A453 - 460
12X-RAY DIFFRACTION12A461 - 516
13X-RAY DIFFRACTION13A517 - 550
14X-RAY DIFFRACTION14A551 - 590
15X-RAY DIFFRACTION15A591 - 596
16X-RAY DIFFRACTION16A597 - 635
17X-RAY DIFFRACTION17A636 - 647
18X-RAY DIFFRACTION18A648 - 666
19X-RAY DIFFRACTION19A667 - 690
20X-RAY DIFFRACTION20A691 - 709

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