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- PDB-2x6x: Tailspike protein mutant D339N of E.coli bacteriophage HK620 in c... -

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Basic information

Entry
Database: PDB / ID: 2x6x
TitleTailspike protein mutant D339N of E.coli bacteriophage HK620 in complex with hexasaccharide
ComponentsTAILSPIKE PROTEIN HK620
KeywordsVIRAL PROTEIN / HYDROLASE
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
Biological speciesSALMONELLA PHAGE HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLorenzen, N.K. / Mueller, J.J. / 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
DepositionFeb 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Feb 5, 2014Group: Database references / Derived calculations / Structure summary
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / 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.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 HK620
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5183
Polymers64,7041
Non-polymers8142
Water10,305572
1
A: TAILSPIKE PROTEIN HK620
hetero molecules

A: TAILSPIKE PROTEIN HK620
hetero molecules

A: TAILSPIKE PROTEIN HK620
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,5549
Polymers194,1133
Non-polymers2,4416
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area25980 Å2
ΔGint-25.8 kcal/mol
Surface area49310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.230, 74.230, 174.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein TAILSPIKE PROTEIN HK620


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: Polysaccharide alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 691.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-6DGlcpa1-4[DGlcpNAcb1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2112h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5][a2211m-1a_1-5]/1-2-3-4/a3-b1_a4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(3+1)][b-D-GlcpNAc]{}[(4+1)][a-D-Glcp]{[(6+1)][a-L-Rhap]{}}}LINUCSPDB-CARE
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.12 Å3/Da / Density % sol: 42.1 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: VAPOR DIFFUSION, HANGING DROP:PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8,2MM EDTA,0.2M NACL.RERVOIR: 100MM TRIS PH8.5,3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICRO LITER, 0.3 MICRO ...Details: VAPOR DIFFUSION, HANGING DROP:PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8,2MM EDTA,0.2M NACL.RERVOIR: 100MM TRIS PH8.5,3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICRO LITER, 0.3 MICRO LITER 33MM HEXASACCHARIDE.TEMPERATURE 20 DEGREE CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2009 / Details: GLAS MIRROR
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: 1.48→37.12 Å / Num. obs: 87697 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 1.48→1.52 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.9 / % possible all: 71.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VJI

2vji


Resolution: 1.48→37.12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.89 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18537 4633 5 %RANDOM
Rwork0.15753 ---
obs0.15894 87697 98.64 %-
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: 17.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.48→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 55 572 5163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214741
X-RAY DIFFRACTIONr_bond_other_d0.0020.023021
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9266464
X-RAY DIFFRACTIONr_angle_other_deg1.13137322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8975597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62124.336226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2615676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9041523
X-RAY DIFFRACTIONr_chiral_restr0.080.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021010
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_it0.72422966
X-RAY DIFFRACTIONr_mcbond_other0.21421236
X-RAY DIFFRACTIONr_mcangle_it1.25734785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0944.51775
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.08861679
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: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 314 -
Rwork0.258 6205 -
obs--95.57 %
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)
12.8285-2.13311.39733.7342-1.75622.24150.12740.4040.0715-0.4279-0.22290.01040.11530.01790.09550.18220.00540.00740.1956-0.02090.015936.669-27.5821-11.2462
20.3432-0.0037-0.41210.27430.58121.7339-0.09680.10980.034-0.12530.00860.0672-0.1231-0.06350.08820.1292-0.0044-0.04820.1392-0.00130.041522.3328-15.08711.7236
30.880.04480.07530.58580.02481.2671-0.08580.0913-0.0247-0.1213-0.01470.0210.0229-0.11470.10040.14060.007-0.04060.1697-0.02160.076918.9711-16.245412.0534
40.23810.0124-0.09340.6911-0.08831.4108-0.02710.08650.0236-0.1518-0.02910.0683-0.1568-0.18080.05620.10980.0517-0.06560.1519-0.01490.080214.8796-8.910517.3648
57.76441.6983-0.70924.6151-1.96395.0297-0.32830.4433-0.2104-0.26230.18220.17620.4523-0.87370.14610.0976-0.0905-0.02550.2531-0.06330.07079.5974-27.047621.954
60.4466-0.0395-0.02080.6502-0.07560.7527-0.04050.0970.0207-0.1086-0.02780.0246-0.0651-0.12920.06830.10870.013-0.04020.14-0.01870.094718.9241-14.760724.6478
70.69570.1083-0.01121.3203-0.29570.8612-0.05710.07250.0284-0.07420.00160.0522-0.1024-0.09530.05550.11690.0225-0.04140.1158-0.0080.091220.3266-9.233530.6977
80.87261.8767-0.55555.2868-2.27931.7550.0463-0.0178-0.1111-0.0432-0.1494-0.2634-0.02510.04970.10310.1027-0.00320.00120.1216-0.02250.119624.8005-25.073933.381
90.33480.2867-0.02590.88280.15930.5429-0.01810.06450.0475-0.048-0.0390.092-0.1234-0.10030.05710.10830.017-0.0290.1141-0.00490.113321.9996-11.025136.2345
100.41490.3258-0.19720.5879-0.03770.6535-0.02430.0628-0.0403-0.0247-0.040.02720.0334-0.11630.06430.0974-0.0036-0.01510.1306-0.01640.122820.8224-19.165840.2455
110.48460.0124-0.19090.72010.05760.4724-0.01410.06580.0027-0.025-0.03090.0707-0.0354-0.11680.04490.09820.0096-0.01760.1148-0.01060.116120.7194-12.302746.2736
120.4180.3089-0.06841.16230.0750.608-0.020.03520.0302-0.0679-0.01370.1358-0.0256-0.09990.03370.1020.0049-0.01350.117-0.00510.137621.4141-12.678653.6203
132.37411.45520.18130.9572-0.21461.80870.0192-0.04170.38960.02450.02190.2816-0.1547-0.2374-0.04110.10260.0215-0.00120.1478-0.00650.233712.5777-13.115260.2331
140.39450.19510.02520.43550.00850.21870.0044-0.01340.0523-0.0144-0.02020.0408-0.0552-0.02650.01580.08810.0044-0.00420.0813-0.00370.132424.8518-9.474765.5975
151.94280.7450.23180.72430.32040.46970.0089-0.05640.03160.0388-0.0160.0119-0.007-0.07110.00710.08890.0030.0010.08620.00310.110825.989-12.305473.1698
160.66040.17780.32830.27060.10980.3304-0.0211-0.05590.08440.0391-0.01020.0688-0.039-0.09030.03130.0791-0.00640.00880.0804-0.00270.129421.6595-15.557678.6442
175.4699-1.65071.91993.0576-0.17741.1163-0.0443-0.1582-0.1690.04330.05570.0871-0.1399-0.0374-0.01150.105-0.00260.0130.0614-0.00280.133832.9185-12.505101.8626
182.28840.7998-0.27981.44490.88440.92840.0341-0.01990.11120.0518-0.060.0872-0.0504-0.09930.0260.12030.0399-0.01030.08010.0170.125827.2506-13.575987.3403
191.12360.86291.261.53091.21151.4931-0.0252-0.0375-0.0239-0.00250.0597-0.028-0.0638-0.022-0.03450.1168-0.00050.00990.0775-0.00130.140236.0471-12.187793.8207
200.0103-0.0508-0.04260.4851-0.00290.4379-0.00270.00190.00130.02860.0293-0.0363-0.04490.0108-0.02660.0858-0.00520.00660.0813-0.00680.134831.4795-13.117292.4233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A112 - 141
2X-RAY DIFFRACTION2A142 - 183
3X-RAY DIFFRACTION3A184 - 226
4X-RAY DIFFRACTION4A227 - 250
5X-RAY DIFFRACTION5A251 - 259
6X-RAY DIFFRACTION6A260 - 323
7X-RAY DIFFRACTION7A324 - 347
8X-RAY DIFFRACTION8A348 - 353
9X-RAY DIFFRACTION9A354 - 379
10X-RAY DIFFRACTION10A380 - 416
11X-RAY DIFFRACTION11A417 - 460
12X-RAY DIFFRACTION12A461 - 524
13X-RAY DIFFRACTION13A525 - 537
14X-RAY DIFFRACTION14A538 - 593
15X-RAY DIFFRACTION15A594 - 616
16X-RAY DIFFRACTION16A617 - 635
17X-RAY DIFFRACTION17A636 - 647
18X-RAY DIFFRACTION18A648 - 665
19X-RAY DIFFRACTION19A666 - 680
20X-RAY DIFFRACTION20A681 - 709

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