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- PDB-6e0w: Crystal structure of the colanidase tailspike protein gp150 of Ph... -

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Basic information

Entry
Database: PDB / ID: 6e0w
TitleCrystal structure of the colanidase tailspike protein gp150 of Phage Phi92 complexed with one repeating unit of colanic acid
ComponentsBacteriophage Phi92 gp150
KeywordsHYDROLASE / Colanidase / tailspike protein / bacteriophage phi92 / colanic acid
Function / homologyParallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / Chem-HLA / Phi92_gp150
Function and homology information
Biological speciesEnterobacteria phage phi92 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsPlattner, M. / Browning, C. / Gerardy-Schahn, R. / Shneider, M.M. / Leiman, P.G. / Schwarzer, D.
CitationJournal: To Be Published
Title: Crystal structure of the colanidase tailspike protein gp150 of Phage Phi92 complexed with one repeating unit of colanic acid
Authors: Browning, C. / Plattner, M. / Shneider, M.M. / Gerardy-Schahn, R. / Leiman, P.G. / Schwarzer, D.
History
DepositionJul 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.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_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophage Phi92 gp150
B: Bacteriophage Phi92 gp150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,14521
Polymers134,7662
Non-polymers3,38019
Water21,2401179
1
A: Bacteriophage Phi92 gp150
hetero molecules

A: Bacteriophage Phi92 gp150
hetero molecules

A: Bacteriophage Phi92 gp150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,50924
Polymers202,1483
Non-polymers4,36021
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 area29400 Å2
ΔGint-227 kcal/mol
Surface area52600 Å2
MethodPISA
2
B: Bacteriophage Phi92 gp150
hetero molecules

B: Bacteriophage Phi92 gp150
hetero molecules

B: Bacteriophage Phi92 gp150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,92739
Polymers202,1483
Non-polymers5,77936
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area33170 Å2
ΔGint-278 kcal/mol
Surface area52420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.623, 117.623, 308.282
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
11B-906-

SO4

21B-906-

SO4

31A-1049-

HOH

41A-1299-

HOH

51A-1382-

HOH

61A-1430-

HOH

71A-1479-

HOH

81A-1559-

HOH

91A-1587-

HOH

101B-1046-

HOH

111B-1104-

HOH

121B-1319-

HOH

131B-1321-

HOH

141B-1336-

HOH

151B-1340-

HOH

161B-1351-

HOH

171B-1400-

HOH

181B-1411-

HOH

191B-1421-

HOH

201B-1452-

HOH

211B-1465-

HOH

221B-1552-

HOH

231B-1571-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Bacteriophage Phi92 gp150


Mass: 67382.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage phi92 (virus) / Gene: PHI92_gene_150, PHI92_150 / Plasmid: pTSL / Production host: Escherichia coli (E. coli) / Strain (production host): B834/DE3 / References: UniProt: I7I026
#2: Polysaccharide beta-D-glucopyranuronic acid-(1-3)-alpha-D-galactopyranose-(1-3)-alpha-L-fucopyranose-(1-4)-alpha-L- ...beta-D-glucopyranuronic acid-(1-3)-alpha-D-galactopyranose-(1-3)-alpha-L-fucopyranose-(1-4)-alpha-L-fucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 810.702 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAb1-3DGalpa1-3LFucpa1-4LFucpa1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5][a2122A-1b_1-5]/1-2-2-3-4/a3-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][a-L-Fucp]{[(4+1)][a-L-Fucp]{[(3+1)][a-D-Galp]{[(3+1)][b-D-GlcpA]{}}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 1196 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-HLA / 1,5-anhydro-4,6-O-[(1R)-1-carboxyethylidene]-D-galactitol


Mass: 234.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14O7
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1179 / 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: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% PEG 8000, 0.2M SrCl2, 0.1M MES pH 6.0, 10mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.8→65 Å / Num. obs: 281287 / % possible obs: 95.8 % / Redundancy: 2.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.096 / Net I/σ(I): 7.47
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 44765 / CC1/2: 0.848 / Rrim(I) all: 0.491 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RMX

4rmx
PDB Unreleased entry


Resolution: 1.803→61.461 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 19.78
RfactorNum. reflection% reflection
Rfree0.1765 2852 1.96 %
Rwork0.1529 --
obs0.1534 280687 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.803→61.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9130 0 212 1179 10521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159606
X-RAY DIFFRACTIONf_angle_d1.17213101
X-RAY DIFFRACTIONf_dihedral_angle_d13.2815539
X-RAY DIFFRACTIONf_chiral_restr0.0861485
X-RAY DIFFRACTIONf_plane_restr0.0081685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8027-1.82320.4091370.41058057X-RAY DIFFRACTION84
1.8232-1.84460.32671570.31279356X-RAY DIFFRACTION97
1.8446-1.86710.29792160.29199367X-RAY DIFFRACTION97
1.8671-1.89080.3141780.25929081X-RAY DIFFRACTION96
1.8908-1.91570.22291680.23929388X-RAY DIFFRACTION97
1.9157-1.94190.25422230.22289282X-RAY DIFFRACTION98
1.9419-1.96960.23912040.21319439X-RAY DIFFRACTION98
1.9696-1.99910.21891980.19399303X-RAY DIFFRACTION98
1.9991-2.03030.17481490.17059473X-RAY DIFFRACTION97
2.0303-2.06360.21911820.17069357X-RAY DIFFRACTION98
2.0636-2.09920.19242440.16259335X-RAY DIFFRACTION98
2.0992-2.13730.2051700.1619324X-RAY DIFFRACTION98
2.1373-2.17840.18892140.18739235X-RAY DIFFRACTION96
2.1784-2.22290.26632200.22498362X-RAY DIFFRACTION88
2.2229-2.27130.24331640.16029329X-RAY DIFFRACTION96
2.2713-2.32410.17671110.15239411X-RAY DIFFRACTION97
2.3241-2.38220.19351770.14239341X-RAY DIFFRACTION98
2.3822-2.44660.15492010.14039414X-RAY DIFFRACTION98
2.4466-2.51860.17791790.15029329X-RAY DIFFRACTION97
2.5186-2.59990.20581580.1798069X-RAY DIFFRACTION84
2.5999-2.69280.18321620.14339303X-RAY DIFFRACTION97
2.6928-2.80070.18722020.14329408X-RAY DIFFRACTION97
2.8007-2.92810.23041450.14929219X-RAY DIFFRACTION96
2.9281-3.08250.16272370.14779204X-RAY DIFFRACTION97
3.0825-3.27560.16131940.14619290X-RAY DIFFRACTION97
3.2756-3.52850.1622030.14119106X-RAY DIFFRACTION96
3.5285-3.88350.1481520.12749201X-RAY DIFFRACTION95
3.8835-4.44530.12511650.11988969X-RAY DIFFRACTION94
4.4453-5.60010.14022220.12149085X-RAY DIFFRACTION94
5.6001-61.49690.15981580.15139160X-RAY DIFFRACTION95
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)
10.0917-0.1012-0.07970.2431-0.04160.19820.0309-0.61950.00590.5014-0.03260.0055-0.0314-0.0878-0.12931.4020.02230.19121.36560.0520.3301-10.304864.7305-18.6986
20.8767-0.02390.08191.1301-0.10981.06140.0136-0.5516-0.14270.52920.06410.2101-0.0008-0.107-0.0540.4373-0.00930.10090.46790.10740.3296-15.210157.7345-54.1236
30.64560.1191-0.31910.7224-0.09321.25610.04380.018-0.0713-0.00960.05680.15580.0437-0.0689-0.10290.1816-0.0054-0.02530.18160.02880.321-12.971459.6719-86.5652
40.27650.2233-0.01632.8988-0.22730.4425-0.03420.0891-0.0862-0.08760.0969-0.06870.0708-0.0028-0.05640.23480.0136-0.02680.2256-0.08290.31353.671142.3626-104.5725
51.66280.2932-0.34761.4858-0.28250.5567-0.0243-0.4658-0.04130.367-0.0277-0.1079-0.01640.12410.040.34370.0084-0.06990.38090.00620.213-49.666532.238919.4896
60.28210.02040.09490.5925-0.09261.129-0.0488-0.02420.06510.0491-0.0382-0.1241-0.0290.11440.0880.187-0.0023-0.03590.23020.03330.358-42.194936.5205-8.9199
71.3187-0.2831-0.28581.29870.36971.1897-0.04620.15650.1163-0.1924-0.0759-0.24-0.08530.19060.09580.1965-0.01580.01960.24770.08590.3216-39.858839.2784-31.8135
81.6567-0.01610.20151.01960.01751.316-0.06190.4195-0.0429-0.3624-0.0744-0.0925-0.04630.1090.13040.3636-0.00210.0890.38810.07160.2717-43.76837.0223-52.7804
92.6881-2.0663-1.58542.1650.21972.67370.17560.1510.8451-1.14130.4673-0.7941-0.50530.278-0.56550.8915-0.06740.17710.74440.00530.6415-54.002857.9993-71.5906
102.1311-2.1263-1.04142.1430.85332.10230.22920.23471.0725-1.42730.4314-0.9892-0.86120.1133-0.55051.1261-0.07610.29830.77010.0850.9004-52.786963.2893-70.9695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 201 through 285 )
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 532 )
3X-RAY DIFFRACTION3chain 'A' and (resid 533 through 675 )
4X-RAY DIFFRACTION4chain 'A' and (resid 676 through 802 )
5X-RAY DIFFRACTION5chain 'B' and (resid 201 through 261 )
6X-RAY DIFFRACTION6chain 'B' and (resid 262 through 424 )
7X-RAY DIFFRACTION7chain 'B' and (resid 425 through 532 )
8X-RAY DIFFRACTION8chain 'B' and (resid 533 through 675 )
9X-RAY DIFFRACTION9chain 'B' and (resid 676 through 765 )
10X-RAY DIFFRACTION10chain 'B' and (resid 766 through 802 )

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