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- PDB-6e0v: Apo crystal structure of the colanidase tailspike protein gp150 o... -

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Basic information

Entry
Database: PDB / ID: 6e0v
TitleApo crystal structure of the colanidase tailspike protein gp150 of Phage Phi92
ComponentsBacteriophage Phi92 gp150
KeywordsHYDROLASE / Colanidase / tailspike protein / bacteriophage phi92
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component
Similarity search - Function
: / Tailspike protein-like, Ig-like domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
STRONTIUM ION / Phi92_gp150
Similarity search - Component
Biological speciesEnterobacteria phage phi92 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLeiman, P.G. / Browning, C. / Gerardy-Schahn, R. / Shneider, M.M. / Plattner, M. / 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
SupersessionJul 17, 2019ID: 4RMX
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)205,80452
Polymers202,1483
Non-polymers3,65549
Water47,2532623
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)205,50948
Polymers202,1483
Non-polymers3,36045
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 area30910 Å2
ΔGint-888 kcal/mol
Surface area52330 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)206,22157
Polymers202,1483
Non-polymers4,07254
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area30930 Å2
ΔGint-640 kcal/mol
Surface area51240 Å2
MethodPISA
3
C: Bacteriophage Phi92 gp150
hetero molecules

C: Bacteriophage Phi92 gp150
hetero molecules

C: Bacteriophage Phi92 gp150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,68151
Polymers202,1483
Non-polymers3,53348
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area27440 Å2
ΔGint-565 kcal/mol
Surface area54960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.400, 118.400, 140.166
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-901-

SR

21A-909-

CL

31B-901-

SR

41B-910-

CL

51C-901-

SR

61C-909-

CL

71A-1150-

HOH

81A-1293-

HOH

91A-1391-

HOH

101A-1392-

HOH

111A-1433-

HOH

121A-1480-

HOH

131A-1499-

HOH

141A-1596-

HOH

151A-1637-

HOH

161A-1658-

HOH

171A-1932-

HOH

181A-1954-

HOH

191B-1053-

HOH

201B-1154-

HOH

211B-1273-

HOH

221B-1428-

HOH

231B-1446-

HOH

241B-1460-

HOH

251B-1475-

HOH

261B-1532-

HOH

271B-1568-

HOH

281B-1584-

HOH

291B-1883-

HOH

301B-1889-

HOH

311B-1896-

HOH

321C-1162-

HOH

331C-1310-

HOH

341C-1321-

HOH

351C-1352-

HOH

361C-1512-

HOH

371C-1637-

HOH

381C-1648-

HOH

391C-1728-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Bacteriophage Phi92 gp150


Mass: 67382.773 Da / Num. of mol.: 3
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

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Non-polymers , 5 types, 2672 molecules

#2: Chemical...
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Sr
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2623 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6 / Details: 10% PEG 8000, 0.2M SrCl2, 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.7679 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7679 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 443661 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.101 / Net I/σ(I): 15.16
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 70838 / CC1/2: 0.685 / Rrim(I) all: 0.975 / % possible all: 98.3

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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: 1.75→48.149 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 16.05
RfactorNum. reflection% reflection
Rfree0.1625 8867 2 %
Rwork0.1339 --
obs0.1345 443591 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.74 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13695 0 113 2623 16431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914242
X-RAY DIFFRACTIONf_angle_d0.9319373
X-RAY DIFFRACTIONf_dihedral_angle_d9.4348257
X-RAY DIFFRACTIONf_chiral_restr0.0642150
X-RAY DIFFRACTIONf_plane_restr0.0062538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7479-1.76780.32582720.279913412X-RAY DIFFRACTION92
1.7678-1.78860.26072960.234314521X-RAY DIFFRACTION100
1.7886-1.81040.26122930.228214373X-RAY DIFFRACTION100
1.8104-1.83330.25912960.216714565X-RAY DIFFRACTION100
1.8333-1.85740.22852980.205514563X-RAY DIFFRACTION100
1.8574-1.88290.21932980.203414546X-RAY DIFFRACTION100
1.8829-1.90980.23432980.186114646X-RAY DIFFRACTION100
1.9098-1.93830.1882960.170214490X-RAY DIFFRACTION100
1.9383-1.96860.18282940.15714446X-RAY DIFFRACTION100
1.9686-2.00090.16912950.149314513X-RAY DIFFRACTION100
2.0009-2.03540.16122980.140814603X-RAY DIFFRACTION100
2.0354-2.07240.17682960.138514486X-RAY DIFFRACTION100
2.0724-2.11220.16853000.137314632X-RAY DIFFRACTION100
2.1122-2.15530.15322960.130914578X-RAY DIFFRACTION100
2.1553-2.20220.16182940.124314414X-RAY DIFFRACTION100
2.2022-2.25340.14432980.123814594X-RAY DIFFRACTION100
2.2534-2.30980.16432940.126114386X-RAY DIFFRACTION100
2.3098-2.37220.16662980.123414566X-RAY DIFFRACTION100
2.3722-2.4420.17552980.127814562X-RAY DIFFRACTION100
2.442-2.52090.14872960.120314596X-RAY DIFFRACTION100
2.5209-2.6110.15882970.118714512X-RAY DIFFRACTION100
2.611-2.71550.14752940.114314422X-RAY DIFFRACTION100
2.7155-2.83910.14142960.114214577X-RAY DIFFRACTION100
2.8391-2.98870.15132960.11414519X-RAY DIFFRACTION100
2.9887-3.17590.14112960.113614521X-RAY DIFFRACTION100
3.1759-3.42110.12852960.114714504X-RAY DIFFRACTION100
3.4211-3.76530.1332980.112214596X-RAY DIFFRACTION100
3.7653-4.30980.13412980.107814553X-RAY DIFFRACTION100
4.3098-5.42870.12732960.105314478X-RAY DIFFRACTION100
5.4287-48.16710.23042960.191614550X-RAY DIFFRACTION100
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)
10.08080.0348-0.10550.0717-0.07210.1333-0.0262-0.25910.09340.2733-0.05-0.1966-0.09060.0262-0.02760.3305-0.0059-0.04160.3046-0.02840.155962.4463-25.4722-14.4471
20.16510.0254-0.00010.1967-0.0710.1819-0.0035-0.03670.04450.05560.0025-0.0063-0.03820.0186-00.1352-0.0035-0.00180.1204-0.02190.130859.3711-16.9508-48.4791
30.0236-0.00020.00640.0466-0.03450.0621-0.0329-0.04060.0506-0.02050.01990.0336-0.0483-0.0344-00.1407-0.0066-0.00330.1243-0.01230.157255.0958-13.6708-70.0267
40.130.0266-0.03040.18380.13910.20410.0126-0.00050.0456-0.01770.00410.0114-0.0058-0.005100.1106-0.00630.00510.11280.00150.112158.748-18.8222-86.3778
50.186-0.13520.08580.11830.03120.16140.02470.04020.015-0.1264-0.01490.0292-0.1308-0.02540.00120.1640.0099-0.02170.17170.01410.143735.3252-24.1282-104.6023
60.2279-0.12360.1520.0953-0.03060.2120.0072-0.1122-0.0061-0.0096-0.01140.0666-0.05970.0067-0.00640.24010.0205-0.05060.189-0.01840.147411.98410.239-89.4469
70.2096-0.0405-0.00650.3954-0.04020.6176-0.03670.01080.0490.0771-0.007-0.1162-0.08280.0932-0.02250.1289-0.0023-0.0290.10180.010.13717.16464.0378-132.1702
80.2484-0.0134-0.12430.1265-0.06260.0911-0.00380.10070.0472-0.13360.0314-0.0039-0.0480.03160.00120.2201-0.003-0.00170.17350.03730.1727.596719.4627-171.5564
90.09110.0755-0.04410.09930.02840.1010.0393-0.2680.13920.0958-0.06240.0306-0.2086-0.0619-0.03480.69640.13920.00720.5256-0.070.002848.840938.89158.8048
100.1727-0.1018-0.01920.0655-0.07780.1741-0.1034-0.14740.11540.39360.0923-0.0666-0.1362-0.0462-0.0150.39480.0463-0.03040.2003-0.00780.165642.243539.0273-16.7644
110.2044-0.0177-0.12670.2343-0.02280.5215-0.00650.0148-0.01490.02530.00590.00840.0082-0.072-0.00470.07930.011-0.01070.08680.01070.16641.788636.5656-49.2721
120.0893-0.09770.11180.3432-0.11470.1899-0.03650.17810.0239-0.03650.2390.46930.0488-0.18990.00940.2084-0.011-0.01830.19610.04030.356343.688713.2618-77.8772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 201 through 261 )
2X-RAY DIFFRACTION2chain 'A' and (resid 262 through 491 )
3X-RAY DIFFRACTION3chain 'A' and (resid 492 through 532 )
4X-RAY DIFFRACTION4chain 'A' and (resid 533 through 675 )
5X-RAY DIFFRACTION5chain 'A' and (resid 676 through 802 )
6X-RAY DIFFRACTION6chain 'B' and (resid 201 through 300 )
7X-RAY DIFFRACTION7chain 'B' and (resid 301 through 632 )
8X-RAY DIFFRACTION8chain 'B' and (resid 633 through 802 )
9X-RAY DIFFRACTION9chain 'C' and (resid 201 through 285 )
10X-RAY DIFFRACTION10chain 'C' and (resid 286 through 410 )
11X-RAY DIFFRACTION11chain 'C' and (resid 411 through 675 )
12X-RAY DIFFRACTION12chain 'C' and (resid 676 through 802 )

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