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- PDB-4urr: Tailspike protein of Sf6 bacteriophage bound to Shigella flexneri... -

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Basic information

Entry
Database: PDB / ID: 4urr
TitleTailspike protein of Sf6 bacteriophage bound to Shigella flexneri O- antigen octasaccharide fragment
ComponentsBIFUNCTIONAL TAIL PROTEIN
KeywordsHYDROLASE / CARBOHYDRATE INTERACTION / TAILSPIKE PROTEIN / 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 / virion attachment to host cell
Similarity search - Function
: / Tailspike protein, C-terminal / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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 ...: / Tailspike protein, C-terminal / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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
: / PHOSPHATE ION / Tail spike protein
Similarity search - Component
Biological speciesSHIGELLA PHAGE SF6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGohlke, U. / Heinemann, U. / Seckler, R. / Barbirz, S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2016
Title: Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein-Polysaccharide Interactions.
Authors: Kang, Y. / Gohlke, U. / Engstrom, O. / Hamark, C. / Scheidt, T. / Kunstmann, S. / Heinemann, U. / Widmalm, G. / Santer, M. / Barbirz, S.
#1: Journal: 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
DepositionJul 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_database_status / struct_conn
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIFUNCTIONAL TAIL PROTEIN
B: BIFUNCTIONAL TAIL PROTEIN
C: BIFUNCTIONAL TAIL PROTEIN
D: BIFUNCTIONAL TAIL PROTEIN
E: BIFUNCTIONAL TAIL PROTEIN
F: BIFUNCTIONAL TAIL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,62931
Polymers329,5826
Non-polymers9,04725
Water27,7251539
1
A: BIFUNCTIONAL TAIL PROTEIN
B: BIFUNCTIONAL TAIL PROTEIN
C: BIFUNCTIONAL TAIL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,28415
Polymers164,7913
Non-polymers4,49312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29750 Å2
ΔGint-12.1 kcal/mol
Surface area44650 Å2
MethodPISA
2
D: BIFUNCTIONAL TAIL PROTEIN
E: BIFUNCTIONAL TAIL PROTEIN
F: BIFUNCTIONAL TAIL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,34616
Polymers164,7913
Non-polymers4,55513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29860 Å2
ΔGint-3.9 kcal/mol
Surface area44720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.987, 138.895, 136.073
Angle α, β, γ (deg.)90.00, 92.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.315701, 0.058398, 0.94706), (0.930904, -0.21231, -0.297224), (0.183713, 0.975456, -0.121389)-13.355, 43.091, -18.412
2given(0.323051, 0.929802, 0.176368), (0.049659, -0.202758, 0.977969), (0.945078, -0.307176, -0.111674)-32.611, 27.503, 23.388
3given(0.331436, 0.929379, 0.162497), (0.013805, -0.17699, 0.984116), (0.943377, -0.323928, -0.071491)-30.385, 35.496, -43.608
4given(0.999933, -0.008693, 0.007645), (0.009041, 0.998868, -0.046698), (-0.00723, 0.046764, 0.99888)2.185, 9.513, -68.584
5given(0.311988, 0.070174, 0.947491), (0.925013, -0.250033, -0.286068), (0.216829, 0.965691, -0.142919)-11.715, 53.129, -84.76

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
BIFUNCTIONAL TAIL PROTEIN / TAILSPIKE-PROTEIN / TSP / ENDORHAMNOSIDASE / ENDO-1 / 3-ALPHA-L-RHAMNOSIDASE


Mass: 54930.371 Da / Num. of mol.: 6 / Fragment: ENDORHAMNOSIDASE DOMAIN, RESIDUES 110-623 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHIGELLA PHAGE SF6 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9XJP3, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide
alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose- ...alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 1301.246 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-3DGlcpNAcb1-2LRhapa1-2LRhapa1-3LRhapa1-3DGlcpNAcb1-2LRhapa1-2LRhapa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,8,7/[a2211m-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-2-1-1-1-2-1/a2-b1_b2-c1_c3-d1_d3-e1_e2-f1_f2-g1_g3-h1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap]{[(2+1)][a-L-Rhap]{[(2+1)][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{[(3+1)][a-L-Rhap]{[(2+1)][a-L-Rhap]{[(2+1)][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{}}}}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1558 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1539 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsALPHA-L-RHAMNOSE (RAM): RAM IS PART OF THE OCTASACCHARIDE LIGAND N-ACETYL-D-GLUCOSAMINE (NAG): NAG ...ALPHA-L-RHAMNOSE (RAM): RAM IS PART OF THE OCTASACCHARIDE LIGAND N-ACETYL-D-GLUCOSAMINE (NAG): NAG IS PART OF THE OCTASACCHARIDE LIGAND

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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: 2.41 Å3/Da / Density % sol: 48.97 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLISED FROM 0.1 M MES, PH 6.5, 16 % PEG 8000, 20 MM MNCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 27, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→46.3 Å / Num. obs: 224609 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 14.29 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 6.2
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VBK

2vbk


Resolution: 1.95→45.33 Å / Cor.coef. Fo:Fc: 0.8972 / Cor.coef. Fo:Fc free: 0.8545 / SU R Cruickshank DPI: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.154
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=48267. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=48267. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=10.
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 11044 4.94 %RANDOM
Rwork0.1957 ---
obs0.1977 223380 99.87 %-
Displacement parametersBiso mean: 18.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.5848 Å20 Å2-0.7726 Å2
2---2.1176 Å20 Å2
3---1.5328 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: LAST / Resolution: 1.95→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22868 0 584 1539 24991
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0147181HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1684877HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10444SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes601HARMONIC2
X-RAY DIFFRACTIONt_gen_planes7081HARMONIC5
X-RAY DIFFRACTIONt_it47181HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.93
X-RAY DIFFRACTIONt_other_torsion14.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3395SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact51566SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2629 763 4.64 %
Rwork0.2204 15690 -
all0.2224 16453 -
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)
10.40690.06430.1820.05870.06030.12350.00210.0505-0.03320.0073-0.0124-0.02640.0287-0.00350.0103-0.0549-0.003-0.0725-0.00930.0102-0.00923.363719.708514.5415
20.31470.10230.17010.12590.14120.1494-0.00460.07370.0402-0.0351-0.0093-0.02380.0086-0.00120.0139-0.0681-0.0476-0.08780.03380.0907-0.00832.019537.4832-0.6901
30.45320.03410.11770.02230.04630.0979-0.00860.04510.0718-0.0034-0.0242-0.016-0.006-0.02220.0329-0.06740.0032-0.0792-0.02850.04070.0232-11.042837.640318.673
40.20220.10840.18310.25540.15740.27270.0103-0.07860.0290.02590.03260.0072-0.0269-0.019-0.0428-0.0435-0.0214-0.02470.0087-0.0876-0.0107-8.891646.1335-48.0407
50.5080.04170.28130.01620.01490.37050.0175-0.0866-0.02920.0164-0.00120.024-0.01380.0583-0.0163-0.0343-0.0023-0.07680.0129-0.0172-0.03094.971128.3217-53.6957
60.38510.0807-0.03490.1098-0.02960.04310.012-0.02990.0686-0.00830.0218-0.0249-0.0415-0.0041-0.0338-0.0764-0.0001-0.0531-0.0322-0.07530.03763.978946.8366-67.3937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

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