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- PDB-2vbk: NATIVE TAILSPIKE PROTEIN OF BACTERIOPHAGE SF6 -

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Basic information

Entry
Database: PDB / ID: 2vbk
TitleNATIVE TAILSPIKE PROTEIN OF BACTERIOPHAGE SF6
ComponentsTAILSPIKE-PROTEIN
KeywordsVIRAL PROTEIN / VIRAL ADHESION PROTEIN / HYDROLASE / TAILSPIKE / ENDORHAMNOSIDASE / RIGHT-HANDED PARALLEL BETA-HELIX
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 / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metabolic process / virion attachment to host cell
Similarity search - Function
: / Tailspike protein, C-terminal / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold ...: / Tailspike protein, C-terminal / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
CARBON DIOXIDE / R-1,2-PROPANEDIOL / PHOSPHATE ION / Tail spike protein
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE SF6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMueller, J.J. / Barbirz, S. / Heinle, K. / Freiberg, A. / Seckler, R. / Heinemann, U.
CitationJournal: Structure / Year: 2008
Title: An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6.
Authors: Muller, J.J. / Barbirz, S. / Heinle, K. / Freiberg, A. / Seckler, R. / Heinemann, U.
History
DepositionSep 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / diffrn_source / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Jan 30, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.2May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.5Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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.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 / _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

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Assembly

Deposited unit
A: TAILSPIKE-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,90428
Polymers55,0321
Non-polymers1,87127
Water11,962664
1
A: TAILSPIKE-PROTEIN
hetero molecules

A: TAILSPIKE-PROTEIN
hetero molecules

A: TAILSPIKE-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,71184
Polymers165,0973
Non-polymers5,61381
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area27290 Å2
ΔGint-104.1 kcal/mol
Surface area54880 Å2
MethodPQS
Unit cell
Length a, b, c (Å)96.231, 96.231, 182.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-623-

MG

21A-624-

MG

31A-2176-

HOH

41A-2641-

HOH

51A-2654-

HOH

61A-2655-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TAILSPIKE-PROTEIN / SF6 TAILSPIKE PROTEIN / TSP


Mass: 55032.414 Da / Num. of mol.: 1
Fragment: RESIDUES 110-623 LACKING THE N-TERMINAL PUTATIVE HEAD-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE SF6 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): D834 / References: UniProt: Q9XJP3

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Non-polymers , 7 types, 691 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN LACKS N-TERMINAL MET AND HAS 622 AA.

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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: 2.9 Å3/Da / Density % sol: 57.7 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION HANGING DROP,20 DEGR. CELSIUS; DROP: 1 MICROL RESERVOIR AND 1 MICROL PROTEIN SOLUTION; RESERVOIR: 0.1M MES, PH6.0,18% PEG8000, 20MM MNCL2; PROTEIN: ...Details: CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION HANGING DROP,20 DEGR. CELSIUS; DROP: 1 MICROL RESERVOIR AND 1 MICROL PROTEIN SOLUTION; RESERVOIR: 0.1M MES, PH6.0,18% PEG8000, 20MM MNCL2; PROTEIN: 10MG/ML, 10MM NA-PHOSPHATE,PH7.0, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.842
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.842 Å / Relative weight: 1
ReflectionResolution: 1.25→20 Å / Num. obs: 169746 / % possible obs: 97.4 % / Redundancy: 2.2 % / Biso Wilson estimate: 9.19 Å2 / Rsym value: 0.05 / Net I/σ(I): 11.6
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.25 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VBE

2vbe


Resolution: 1.25→14.92 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.478 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PROTEIN ATOM OCCUPANCIES LESS THAN 1.0 AND FOR WHICH NO ALTERNATE LOCATION ATOM RECORD IS PROVIDED ARE MOSTLY DUE TO RADIATION DAMAGES.
RfactorNum. reflection% reflectionSelection details
Rfree0.142 8511 5 %RANDOM
Rwork0.119 ---
obs0.12 161221 97.4 %-
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: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.25→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3833 0 117 664 4614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214302
X-RAY DIFFRACTIONr_bond_other_d0.0010.023771
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9525877
X-RAY DIFFRACTIONr_angle_other_deg2.38938847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024931
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02837
X-RAY DIFFRACTIONr_nbd_refined0.2070.2775
X-RAY DIFFRACTIONr_nbd_other0.2770.24411
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.22267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2427
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.246
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.2169
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.276
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.87932704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.41564413
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.25651598
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3467.51435
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: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.227 548
Rwork0.194 10251

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