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- PDB-5mf2: Bacteriophage T5 distal tail protein pb9 co-crystallized with Tb-Xo4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5mf2
TitleBacteriophage T5 distal tail protein pb9 co-crystallized with Tb-Xo4
ComponentsDistal tail protein
KeywordsVIRAL PROTEIN / Lanthanide complexes / Crystallogenesis / Anomalous scattering / Bacteriophages
Function / homology
Function and homology information


virus tail, baseplate / virus tail
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #290 / Phosphorylase Kinase; domain 1 - #190 / : / : / : / Distal tail protein pb9, A domain C-terminal / Distal tail protein pb9, A domain, N-terminal / Distal tail protein pb9, B domain / Elongation Factor Tu (Ef-tu); domain 3 / Phosphorylase Kinase; domain 1 ...Elongation Factor Tu (Ef-tu); domain 3 - #290 / Phosphorylase Kinase; domain 1 - #190 / : / : / : / Distal tail protein pb9, A domain C-terminal / Distal tail protein pb9, A domain, N-terminal / Distal tail protein pb9, B domain / Elongation Factor Tu (Ef-tu); domain 3 / Phosphorylase Kinase; domain 1 / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tb-Xo4 / TERBIUM(III) ION / Distal tail protein pb9
Similarity search - Component
Biological speciesEscherichia phage T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsEngilberge, S. / Riobe, F. / Di Pietro, S. / Lassalle, L. / Arnaud, C.-A. / Breyton, C. / Madern, D. / Coquelle, N. / Maury, O. / Girard, E.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BS07-0007-01 France
Citation
Journal: Chem Sci / Year: 2017
Title: Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence.
Authors: Engilberge, S. / Riobe, F. / Di Pietro, S. / Lassalle, L. / Coquelle, N. / Arnaud, C.A. / Pitrat, D. / Mulatier, J.C. / Madern, D. / Breyton, C. / Maury, O. / Girard, E.
#1: Journal: J. Virol. / Year: 2014
Title: Crystal structure of pb9, the distal tail protein of bacteriophage T5: a conserved structural motif among all siphophages.
Authors: Flayhan, A. / Vellieux, F.M. / Lurz, R. / Maury, O. / Contreras-Martel, C. / Girard, E. / Boulanger, P. / Breyton, C.
History
DepositionNov 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 25, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_conn_angle
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 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value
Revision 2.1May 29, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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: Distal tail protein
B: Distal tail protein
C: Distal tail protein
D: Distal tail protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,63623
Polymers97,9184
Non-polymers3,71819
Water5,368298
1
A: Distal tail protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5837
Polymers24,4791
Non-polymers1,1046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Distal tail protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3107
Polymers24,4791
Non-polymers8306
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Distal tail protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3544
Polymers24,4791
Non-polymers8743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Distal tail protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3895
Polymers24,4791
Non-polymers9104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.464, 95.502, 71.492
Angle α, β, γ (deg.)90.00, 103.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Distal tail protein / Dit / Tail protein pb9


Mass: 24479.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: D16, ORF128, T5.139, T5p135 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6QGE8
#2: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 6 to 11 % PEG 6000 and MPD 5% in 100 mM HEPES buffer pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.64 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.64 Å / Relative weight: 1
ReflectionResolution: 2→48.384 Å / Num. obs: 122847 / % possible obs: 99.4 % / Redundancy: 6.5 % / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementResolution: 2→48.38 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 27.36
RfactorNum. reflection% reflection
Rfree0.236 6108 4.97 %
Rwork0.21 --
obs0.211 122847 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 106 298 6188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036029
X-RAY DIFFRACTIONf_angle_d0.5968194
X-RAY DIFFRACTIONf_dihedral_angle_d12.0273526
X-RAY DIFFRACTIONf_chiral_restr0.046886
X-RAY DIFFRACTIONf_plane_restr0.0031057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.34372060.36553784X-RAY DIFFRACTION96
2.0227-2.04650.35262080.34993860X-RAY DIFFRACTION98
2.0465-2.07150.36042040.34453831X-RAY DIFFRACTION98
2.0715-2.09770.35962030.33053958X-RAY DIFFRACTION98
2.0977-2.12530.32852030.32053819X-RAY DIFFRACTION99
2.1253-2.15440.33722050.31033896X-RAY DIFFRACTION99
2.1544-2.18520.29632050.29063819X-RAY DIFFRACTION99
2.1852-2.21780.2992110.27834003X-RAY DIFFRACTION99
2.2178-2.25250.29391980.27393854X-RAY DIFFRACTION99
2.2525-2.28940.30242140.27953940X-RAY DIFFRACTION99
2.2894-2.32890.26312040.26973849X-RAY DIFFRACTION99
2.3289-2.37120.28132110.2723891X-RAY DIFFRACTION98
2.3712-2.41680.31842070.25783789X-RAY DIFFRACTION98
2.4168-2.46620.28791930.24723977X-RAY DIFFRACTION99
2.4662-2.51980.30622120.24223900X-RAY DIFFRACTION99
2.5198-2.57840.27012070.2413944X-RAY DIFFRACTION99
2.5784-2.64290.29492010.23483878X-RAY DIFFRACTION99
2.6429-2.71430.26911990.22083898X-RAY DIFFRACTION99
2.7143-2.79420.23672080.2173822X-RAY DIFFRACTION99
2.7942-2.88440.29322040.21593960X-RAY DIFFRACTION99
2.8844-2.98750.24182090.21663874X-RAY DIFFRACTION99
2.9875-3.10710.23541900.20183938X-RAY DIFFRACTION100
3.1071-3.24840.21862060.1983914X-RAY DIFFRACTION99
3.2484-3.41970.24971990.19183939X-RAY DIFFRACTION100
3.4197-3.63380.20542010.17643870X-RAY DIFFRACTION99
3.6338-3.91430.1642000.16993875X-RAY DIFFRACTION99
3.9143-4.3080.19762000.16853883X-RAY DIFFRACTION98
4.308-4.93080.17082040.14833925X-RAY DIFFRACTION100
4.9308-6.21030.19452000.18343932X-RAY DIFFRACTION100
6.2103-48.39770.22571960.21743917X-RAY DIFFRACTION99
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)
18.9019-6.26245.8045.8199-5.32599.00440.10960.3625-0.3431-0.1894-0.09490.5307-0.29380.141-0.0430.3714-0.0320.04390.30920.02190.343130.924313.6978-1.5329
29.50214.21412.3754.74595.0436.12720.0657-0.0356-0.30760.40760.0293-0.27250.68941.0967-0.06470.30650.005-0.01380.33050.03040.410535.86091.379216.7534
35.77683.7508-0.64655.2482-1.62397.9170.00990.17910.3414-0.078-0.2344-0.2337-0.35020.48740.08460.30140.0004-0.01250.31060.03120.346338.658514.75970.2089
46.51780.48881.50062.18720.75187.75830.08030.1639-0.08290.03850.2005-0.0657-0.2689-0.0572-0.22630.3414-0.09340.03420.26840.020.268415.859711.557920.0361
54.8031-0.2184-3.12070.93560.04785.48260.1678-0.12670.04680.0678-0.1291-0.1346-0.25810.468-0.07740.3073-0.0555-0.02050.23020.02170.252224.16149.412320.4069
67.7485-1.1398-2.68684.2857-1.82132.4336-0.13670.3054-0.3821-0.3347-0.4922-0.1742-0.21141.76520.40060.3182-0.14040.0430.44040.01440.501641.59687.7339-0.6383
75.29524.10764.79845.87994.43864.57240.0912-0.494-0.2432-0.6024-0.11780.3682-0.0648-0.5192-0.1460.3353-0.06970.03280.39120.06810.43473.26-17.23821.3506
84.28061.62370.29893.756-1.31422.68420.2572-0.5206-0.41660.18940.02310.26330.3892-0.6155-0.19170.39-0.06520.01490.48340.10150.41045.4095-17.031129.2048
95.8317-2.31272.96782.6246-1.57356.3001-0.05280.2513-0.09070.17830.02590.2284-0.1711-0.01450.06690.2969-0.05170.04060.2970.04450.380226.6255-15.586111.6322
104.07390.4138-1.96680.8958-0.64653.24430.0116-0.1623-0.09070.04960.00820.002-0.10390.0333-0.00390.3011-0.0178-0.00980.27220.02660.32726.428-13.269218.2182
119.6299-0.3159-4.33992.8762.56834.01260.1763-2.9772-0.12931.07490.1557-0.44570.60621.503-0.21480.4877-0.09670.03230.7670.16370.546312.1015-15.996933.4795
122.86940.3931-2.62218.37940.17214.86290.4292-1.17650.24910.3858-0.28190.7899-0.2716-1.0729-0.1710.4296-0.09620.07850.58930.02210.33853.776-12.512830.8427
136.46424.68663.8353.52542.93795.6116-0.2282-0.20470.2165-0.564-0.0659-0.6042-0.51640.04510.31650.4910.05820.09020.3703-0.01470.3852-5.661813.651865.1938
145.0608-1.0067-1.74216.8445-4.94164.9124-0.13270.1284-0.5942-0.1836-0.0819-0.27630.6971-0.83280.24020.2958-0.12470.03410.4136-0.010.3433-6.1536-1.917852.5403
154.9681-0.0740.46145.45545.06918.44520.10530.12360.5764-0.5684-0.17480.4011-1.039-0.81860.05350.44530.0483-0.00830.54580.06610.4893-14.66811.852163.7738
165.9549-0.923-3.30710.99952.46486.29110.1355-1.0630.2752-0.00810.1298-0.0886-0.09970.9431-0.28120.3704-0.0163-0.00880.4496-0.14660.30847.478112.387351.2787
175.54330.5996-2.66630.9723-0.88795.90970.1983-0.0666-0.0530.1027-0.0638-0.0179-0.1065-0.1885-0.16050.3645-0.04890.00580.2614-0.0330.25055.91158.042341.2621
187.64671.5369-1.99364.74482.48592.9670.1140.2458-0.1912-0.0164-0.06860.09650.4015-0.9234-0.10670.2547-0.03250.00180.40080.09040.4073-14.93964.01363.159
194.5322-2.77264.73178.6804-4.39126.37060.44670.1236-0.95930.0455-0.4907-0.00270.770.3767-0.02040.26620.0210.02150.3853-0.0080.475275.2752-18.75440.7726
207.2072.12884.01718.47421.8488.67370.22170.04630.82430.2092-0.07860.1530.0246-0.0897-0.13120.2905-0.12880.09150.43430.06270.336865.0736-2.6663-1.6625
217.3659-2.6913-1.22513.5178-1.02863.01460.17370.6407-0.6441-0.1678-0.2890.21790.6313-0.10670.12560.3635-0.08150.00050.5575-0.10110.479875.7325-16.0274-7.1787
224.5621.96830.85672.4759-1.63096.3374-0.1249-0.3228-0.61020.15720.1504-0.21980.03130.16260.02220.26660.05550.03990.3959-0.05090.436950.8807-15.423311.0676
235.30010.2516-2.79541.0307-0.50034.1499-0.13190.1827-0.00640.0263-0.08-0.0530.02690.03320.18870.2731-0.023-0.01420.40890.00750.426151.0997-11.45255.3985
246.141-2.98031.35564.3827-0.15855.03290.11860.76150.1254-0.2365-0.16080.04510.00130.06780.05960.353-0.12690.05150.56740.0940.37376.1994-8.1562-8.2205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:21)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 22:49)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 50:84)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 85:122)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 123:178)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 179:205)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 1:23)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 24:84)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 85:122)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 123:173)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 174:178)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 179:205)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 1:18)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 19:52)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 53:81)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 82:99)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 100:173)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 174:205)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 1:17)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 18:53)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 54:84)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 85:122)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 123:173)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 174:205)

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