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- PDB-3u6x: Phage TP901-1 baseplate tripod -

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Basic information

Entry
Database: PDB / ID: 3u6x
TitlePhage TP901-1 baseplate tripod
Components
  • BPP
  • ORF48
KeywordsVIRAL PROTEIN / helix/beta / receptor binding complex / phage tail baseplate
Function / homology
Function and homology information


virus tail, baseplate / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Immunoglobulin-like - #3320 / Baseplate upper protein, immunoglobulin like domain / Baseplate upper protein immunoglobulin like domain / Helix Hairpins - #2190 / BppU, N-terminal / BppU N-terminal domain / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Phage tail base-plate Siphoviridae RBP, head domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head ...Immunoglobulin-like - #3320 / Baseplate upper protein, immunoglobulin like domain / Baseplate upper protein immunoglobulin like domain / Helix Hairpins - #2190 / BppU, N-terminal / BppU N-terminal domain / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Phage tail base-plate Siphoviridae RBP, head domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Adenovirus pIV-like, attachment domain / Helix Hairpins / Helix non-globular / Special / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / ORF48 / BPP
Similarity search - Component
Biological speciesLactococcus phage TP901-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVeesler, D. / Spinelli, S. / Mahony, J. / Lichiere, J. / Blangy, S. / Bricogne, G. / Legrand, P. / Ortiz-Lombardia, M. / Campanacci, V.I. / van Sinderen, D. / Cambillau, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism.
Authors: Veesler, D. / Spinelli, S. / Mahony, J. / Lichiere, J. / Blangy, S. / Bricogne, G. / Legrand, P. / Ortiz-Lombardia, M. / Campanacci, V. / van Sinderen, D. / Cambillau, C.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BPP
B: BPP
C: BPP
D: BPP
E: BPP
F: BPP
G: BPP
H: BPP
I: BPP
J: BPP
K: BPP
L: BPP
M: BPP
N: BPP
O: BPP
P: BPP
Q: BPP
R: BPP
S: ORF48
T: ORF48
U: ORF48
X: ORF48
Y: ORF48
Z: ORF48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,56042
Polymers381,12224
Non-polymers1,43818
Water62,9083492
1
A: BPP
B: BPP
C: BPP
D: BPP
E: BPP
F: BPP
G: BPP
H: BPP
I: BPP
X: ORF48
Y: ORF48
Z: ORF48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,36022
Polymers190,56112
Non-polymers79910
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: BPP
K: BPP
L: BPP
M: BPP
N: BPP
O: BPP
P: BPP
Q: BPP
R: BPP
S: ORF48
T: ORF48
U: ORF48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,20020
Polymers190,56112
Non-polymers6398
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.960, 237.420, 152.210
Angle α, β, γ (deg.)90.00, 115.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BPP / Baseplate protein


Mass: 17303.387 Da / Num. of mol.: 18 / Fragment: ORF49
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: bpp, ORF49 / Plasmid: pET22AGW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLys / References: UniProt: Q9G096
#2: Protein
ORF48


Mass: 11610.187 Da / Num. of mol.: 6 / Fragment: ORF48 195-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: ORF48 / Plasmid: pET22AGW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLys / References: UniProt: Q9AZ56
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3492 / 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: 6.41 Å3/Da / Density % sol: 80.8 %
Crystal growTemperature: 273 K / pH: 7.2
Details: Concentration of tripod: 5.3 mg/ml, 25% PEG1000, 0.1 M HEPES pH 7.2, , VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2011 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 298571 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 53.18 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 10.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.55 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.48 / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EJC

3ejc


Resolution: 2.6→49.74 Å / Cor.coef. Fo:Fc: 0.8801 / Cor.coef. Fo:Fc free: 0.8602 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 28781 9.98 %RANDOM
Rwork0.1784 ---
obs0.1812 288313 --
all-288313 --
Displacement parametersBiso mean: 49.68 Å2
Baniso -1Baniso -2Baniso -3
1--24.157 Å20 Å2-1.1568 Å2
2--25.9395 Å20 Å2
3----1.7825 Å2
Refine analyzeLuzzati coordinate error obs: 0.315 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26570 0 18 3492 30080
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0127086HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2336685HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9177SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes599HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3990HARMONIC5
X-RAY DIFFRACTIONt_it27086HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion19.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion03648SEMIHARMONIC5
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_contact030299SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2709 2172 10.17 %
Rwork0.23 19190 -
all0.2341 21362 -
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)
10.21630.1519-0.21690.16270.1923-0.0336-0.01250.0170.00890.0088-0.0012-0.00520.0081-0.00390.0137-0.00930.00570.0214-0.01940.02450.0108-92.4296-3.82167.3598
20.29760.5006-0.26580.2349-0.1885-0.1819-0.01110.0160.0178-0.00140.00430.00290.0111-0.01510.0068-0.01950.00080.0289-0.02330.02770.0195-105.5344-3.366458.918
30.13920.0585-0.13820.19760.261-0.02720.0010.0170.00640.00060.00810.00030.00790.0052-0.0092-0.0204-0.02380.0386-0.01970.00920.0168-91.7663-4.822451.8855
4-0.03440.11560.01050.282-0.15110.1053-0.0185-0.0116-0.01230.009-0.0089-0.00430.01240.0150.02750.03940.0163-0.0237-0.0082-0.0252-0.0404-64.9232-5.990828.6452
5-0.0780.21930.04330.17670.05790.1576-0.00340.0141-0.00560.0016-0.00320.00260.0060.01240.00660.0239-0.01350-0.0094-0.0023-0.0318-77.8013-3.277920.4052
6-0.0420.04150.07840.26890.54540.1879-0.00790.00050.00310.00440.0021-0.00520.00840.01160.00580.024-0.0076-0.0051-0.0081-0.016-0.0333-64.0264-4.880513.1751
70.236-0.50470.30740.13590.51660.241-0.0195-0.0141-0.00040.0006-0.0031-0.00260.02060.01280.0226-0.01540.013-0.0334-0.0011-0.0151-0.0024-45.1048-7.584472.0377
80.0240.13080.11010.18530.56150.1002-0.02230.00640.0141-0.00210.00660.00090.0257-0.01510.0156-0.02320.0255-0.0232-0.01030.02320.0227-58.0972-7.398663.5252
90.15410.38850.10820.0054-0.11550.0684-0.01360.01580.0029-0.00090.0007-0.0040.01690.00770.0129-0.01450.0054-0.0303-0.0037-0.00530.0019-44.2653-6.343756.4953
10-0.0744-0.05740.03810.2209-0.62870.2354-0.0024-0.01470.0022-0.00060.00450.00180.0075-0.0084-0.00210.033-0.0171-0.0066-0.00830.036-0.031-80.961668.9337.7982
11-0.1009-0.06130.08080.38810.1870.1009-0.0263-0.01760.01460.0019-0.00130.00920.0132-0.00970.02750.02990.01110.0052-0.01270.0451-0.0299-77.941370.490822.9356
12-0.1435-0.06820.13130.2317-0.05550.1921-0.00540.00670.0019-0.0048-0.0014-0.0068-0.0016-0.01810.00670.0164-0.01740.0061-0.009-0.0117-0.0029-66.187169.496612.8289
130.2937-0.5759-0.18910.29310.1972-0.102-0.0104-0.00350.00520.00570.0029-0.00290.01760.00240.00740.00290.00420.0309-0.0269-0.00210.0012-91.105470.56768.7385
140.07380.0969-0.07380.4119-0.3461-0.01240.0004-0.009-0.00650.0024-0.0026-0.0051-0.00110.00860.0022-0.00780.00460.0307-0.0171-0.02510.0257-79.499871.534258.4711
150.1938-0.0961-0.19180.3105-0.2469-0.0408-0.0052-0.02210.0031-0.0008-0.00120.00110.00640.01290.0064-0.00440.02030.0393-0.02120.01520.0028-93.962168.968853.4862
160.2933-0.32980.04970.14581.5415-0.0199-0.0229-0.0002-0.0219-0.0062-0.0064-0.00380.04210.01660.0293-0.03560.001-0.0105-0.0055-0.01570.0182-33.135673.520346.9863
170.1713-0.45140.08060.21040.36230.0379-0.01390.0075-0.0138-0.0034-0.0012-0.00590.02870.00220.0151-0.006-0.0288-0.0166-0.0062-0.01940.008-47.859773.131442.0237
180.02990.27590.13680.0818-0.77870.1246-0.0101-0.0051-0.01660.00380.0001-0.00110.02760.01320.01-0.0179-0.0007-0.0215-0.00910.00350.0089-44.878472.243657.2063
190.62380.1070.16400.17670.35230.000500.0019-0.00380.00040.00920.00010.0005-0.00090.005-0.0008-0.00540.0253-0.0083-0.0121-83.9946132.58926.4571
200.81190.1014-0.29790.2223-0.23190.29270.00180.0003-0.00040.0001-0.0017-0.0073-0.00230.00050-0.0036-0.0091-0.02040.0348-0.0077-0.0145-56.1581134.52235.4227
210.14890.14040.0620.18340.44650.47350.000400.00120.0098-0.00040.0078-0.00340.00610-0.0042-0.01430.01010.0194-0.00650.0022-77.9161133.84655.0896
220.16580.024-0.1130.1845-0.0603-0.00070.0004-0.0014-0.00020.00740.0018-0.00550.0016-0.0033-0.00210.01420.01120.003-0.00270.002-0.0018-67.8561-68.809361.3879
23-0.034-0.19180.03220.27330.04350.17990.00010.0003-0.001-0.0034-0.0002-0.0047-0.00090.00120.00020.015-0.00090.0102-0.0009-0.0082-0.0012-66.3036-68.027432.0873
240.1255-0.0422-0.15050.6260.17550.0832-0.00010.0071-0.00080.0028-0.00130.00690.00170.00020.0014-0.0016-0.00280.0307-0.0049-0.00510.0103-92.424-66.881945.434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 163}A2 - 163
2X-RAY DIFFRACTION2{B|2 - 163}B2 - 163
3X-RAY DIFFRACTION3{C|2 - 163}C2 - 163
4X-RAY DIFFRACTION4{D|2 - 163}D2 - 163
5X-RAY DIFFRACTION5{E|2 - 163}E2 - 163
6X-RAY DIFFRACTION6{F|2 - 163}F2 - 163
7X-RAY DIFFRACTION7{G|2 - 163}G2 - 163
8X-RAY DIFFRACTION8{H|2 - 163}H2 - 163
9X-RAY DIFFRACTION9{I|2 - 163}I2 - 163
10X-RAY DIFFRACTION10{J|2 - 163}J2 - 163
11X-RAY DIFFRACTION11{K|2 - 163}K2 - 163
12X-RAY DIFFRACTION12{L|2 - 163}L2 - 163
13X-RAY DIFFRACTION13{M|2 - 163}M2 - 163
14X-RAY DIFFRACTION14{N|2 - 163}N2 - 163
15X-RAY DIFFRACTION15{O|2 - 163}O2 - 163
16X-RAY DIFFRACTION16{P|2 - 163}P2 - 163
17X-RAY DIFFRACTION17{Q|2 - 163}Q2 - 163
18X-RAY DIFFRACTION18{R|2 - 163}R2 - 163
19X-RAY DIFFRACTION19{S|195 - 299}S195 - 299
20X-RAY DIFFRACTION20{T|195 - 299}T195 - 299
21X-RAY DIFFRACTION21{U|195 - 299}U195 - 299
22X-RAY DIFFRACTION22{X|195 - 299}X195 - 299
23X-RAY DIFFRACTION23{Y|195 - 299}Y195 - 299
24X-RAY DIFFRACTION24{Z|195 - 299}Z195 - 299

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