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- PDB-2x8k: Crystal Structure of SPP1 Dit (gp 19.1) Protein, a Paradigm of Hu... -

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Entry
Database: PDB / ID: 2x8k
TitleCrystal Structure of SPP1 Dit (gp 19.1) Protein, a Paradigm of Hub Adsorption Apparatus in Gram-positive Infecting Phages.
ComponentsHYPOTHETICAL PROTEIN 19.1
KeywordsVIRAL PROTEIN / DISTAL TAIL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #200 / Jelly Rolls - #860 / Rhinovirus 14, subunit 4 - #30 / : / Siphovirus-type tail component, C-terminal domain / Distal tail protein, N-terminal / Siphovirus-type tail component / Phage tail protein RIFT-related domain / Rhinovirus 14, subunit 4 / Other non-globular ...Elongation Factor Tu (Ef-tu); domain 3 - #200 / Jelly Rolls - #860 / Rhinovirus 14, subunit 4 - #30 / : / Siphovirus-type tail component, C-terminal domain / Distal tail protein, N-terminal / Siphovirus-type tail component / Phage tail protein RIFT-related domain / Rhinovirus 14, subunit 4 / Other non-globular / Elongation Factor Tu (Ef-tu); domain 3 / Special / Jelly Rolls / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBACILLUS PHAGE SPP1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsVeesler, D. / Robin, G. / Lichiere, J. / Auzat, I. / Tavares, P. / Bron, P. / Campanacci, V. / Cambillau, C.
CitationJournal: J Biol Chem / Year: 2010
Title: Crystal structure of bacteriophage SPP1 distal tail protein (gp19.1): a baseplate hub paradigm in gram-positive infecting phages.
Authors: David Veesler / Gautier Robin / Julie Lichière / Isabelle Auzat / Paulo Tavares / Patrick Bron / Valérie Campanacci / Christian Cambillau /
Abstract: Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most ...Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most orf products belonging to these regions. We report here the structure of the SPP1 distal tail protein (Dit, gp19.1). The combination of x-ray crystallography, EM, and light scattering established that Dit is a back-to-back dimer of hexamers. However, Dit fitting in the virion EM maps was only possible with a hexamer located between the tail-tube and the tail-tip. Structure comparison revealed high similarity between Dit and a central component of lactophage baseplates. Sequence similarity search expanded its relatedness to several phage proteins, suggesting that Dit is a docking platform for the tail adsorption apparatus in Siphoviridae infecting gram-positive bacteria and that its architecture is a paradigm for these hub proteins. Dit structural similarity extends also to non-contractile and contractile phage tail proteins (gpV(N) and XkdM) as well as to components of the bacterial type 6 secretion system, supporting an evolutionary connection between all these devices.
History
DepositionMar 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN 19.1
B: HYPOTHETICAL PROTEIN 19.1
C: HYPOTHETICAL PROTEIN 19.1


Theoretical massNumber of molelcules
Total (without water)85,2873
Polymers85,2873
Non-polymers00
Water00
1
A: HYPOTHETICAL PROTEIN 19.1
B: HYPOTHETICAL PROTEIN 19.1
C: HYPOTHETICAL PROTEIN 19.1

A: HYPOTHETICAL PROTEIN 19.1
B: HYPOTHETICAL PROTEIN 19.1
C: HYPOTHETICAL PROTEIN 19.1

A: HYPOTHETICAL PROTEIN 19.1
B: HYPOTHETICAL PROTEIN 19.1
C: HYPOTHETICAL PROTEIN 19.1

A: HYPOTHETICAL PROTEIN 19.1
B: HYPOTHETICAL PROTEIN 19.1
C: HYPOTHETICAL PROTEIN 19.1


Theoretical massNumber of molelcules
Total (without water)341,14812
Polymers341,14812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area38060 Å2
ΔGint-145.9 kcal/mol
Surface area129290 Å2
MethodPISA
2
A: HYPOTHETICAL PROTEIN 19.1
B: HYPOTHETICAL PROTEIN 19.1
C: HYPOTHETICAL PROTEIN 19.1

A: HYPOTHETICAL PROTEIN 19.1
B: HYPOTHETICAL PROTEIN 19.1
C: HYPOTHETICAL PROTEIN 19.1

A: HYPOTHETICAL PROTEIN 19.1
B: HYPOTHETICAL PROTEIN 19.1
C: HYPOTHETICAL PROTEIN 19.1

A: HYPOTHETICAL PROTEIN 19.1
B: HYPOTHETICAL PROTEIN 19.1
C: HYPOTHETICAL PROTEIN 19.1


Theoretical massNumber of molelcules
Total (without water)341,14812
Polymers341,14812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area34130 Å2
ΔGint-138.4 kcal/mol
Surface area133230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.188, 125.745, 189.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9963, -0.000962, 0.1519), (-0.06412, 0.4768, 1.319), (-0.02362, -0.5837, 0.475)
Vector: -0.06303, -0.3761, 0.5599)

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Components

#1: Protein HYPOTHETICAL PROTEIN 19.1


Mass: 28429.014 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS PHAGE SPP1 (virus) / Plasmid: PETG20A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): T7 EXPRESS IQ PLYSS / References: UniProt: O48459

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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: 3.99 Å3/Da / Density % sol: 68.94 % / Description: NONE
Crystal growDetails: 2 M NACL, 0.1 M NA ACETATE PH 4.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSOLEIL PROXIMA 110.98
SYNCHROTRONESRF BM1420.9782
Detector
TypeIDDetectorDate
ADSC CCD1CCDJul 18, 2009
MARRESEARCH2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.97821
ReflectionResolution: 2.95→104.83 Å / Num. obs: 27345 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 98.11 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→34.37 Å / Cor.coef. Fo:Fc: 0.9251 / Cor.coef. Fo:Fc free: 0.9039 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.354 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 958 3.53 %RANDOM
Rwork0.2003 ---
obs0.2016 27167 --
Displacement parametersBiso mean: 109.39 Å2
Baniso -1Baniso -2Baniso -3
1--25.5238 Å20 Å20 Å2
2--8.4807 Å20 Å2
3---17.0431 Å2
Refine analyzeLuzzati coordinate error obs: 0.563 Å
Refinement stepCycle: LAST / Resolution: 2.95→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5710 0 0 0 5710
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0135821HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.267924HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1967SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes146HARMONIC2
X-RAY DIFFRACTIONt_gen_planes841HARMONIC5
X-RAY DIFFRACTIONt_it5821HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion24.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion801SEMIHARMONIC5
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_contact6414SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.06 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3005 97 3.4 %
Rwork0.2487 2755 -
all0.2505 2852 -
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)
11.10980.2763-0.25882.9824-0.66453.2415-0.05730.1716-0.1158-0.6493-0.09870.15210.4348-0.22290.1561-0.0845-0.0369-0.1089-0.1044-0.0537-0.156236.512844.324773.8835
24.37481.50090.53780-0.59442.96830.10930.4318-0.9939-0.42270.49660.47250.4177-0.5075-0.60590.3698-0.209-0.3691-0.3741-0.02270.348921.887813.558572.1476
37.16612.66532.44982.1010.38054.70780.16360.3841-0.3321-0.01880.34881.22310.0822-1.3454-0.51250.0645-0.1919-0.1857-0.20570.05330.293916.605216.350671.5926
40.8283-0.1386-0.0622.88061.01533.16730.05820.1583-0.1370.0084-0.24290.4030.7829-0.04020.18470.0205-0.06370.1067-0.10050.0528-0.179736.422535.6708100.145
53.98780.7287-1.29324.50150.17681.3042-0.3652-0.1539-0.3486-1.03770.29940.53690.7735-0.6580.06580.2402-0.3730.1486-0.20490.2061-0.340921.136820.4548127.277
65.71582.5974-2.05425.9576-0.81053.9732-0.32760.8320.2487-1.0080.62341.37990.8627-0.91-0.29580.2549-0.3129-0.0687-0.1450.2391-0.136815.270622.4126125.927
70.7104-0.2481-0.01633.8330.31662.59410.06590.09010.1843-0.59070.11070.4028-0.4929-0.0528-0.1766-0.03460.0349-0.2064-0.0657-0.0603-0.20536.547371.550868.5268
85.1802-1.592-1.63420-3.78440-0.05591.6096-0.5336-0.5206-0.14810.3024-0.8629-0.63080.2040.34210.2646-0.45590.3516-0.3722-0.363321.126257.249941.9274
97.2295-0.31111.73231.464-0.73381.1455-0.02381.11090.2107-0.2052-0.29550.9557-1.0149-1.29610.31920.16980.4166-0.45590.5832-0.3622-0.177515.779958.553744.6572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A9 - A135)
2X-RAY DIFFRACTION2(A136 - A180)
3X-RAY DIFFRACTION3(A181 - A253)
4X-RAY DIFFRACTION4(B9 - B135)
5X-RAY DIFFRACTION5(B136 - B180)
6X-RAY DIFFRACTION6(B181 - B253)
7X-RAY DIFFRACTION7(C9 - C135)
8X-RAY DIFFRACTION8(C136 - C180)
9X-RAY DIFFRACTION9(C181 - C253)

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