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- PDB-3uh8: N-terminal domain of phage TP901-1 ORF48 -

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Basic information

Entry
Database: PDB / ID: 3uh8
TitleN-terminal domain of phage TP901-1 ORF48
ComponentsORF48
KeywordsVIRAL PROTEIN / all beta protein / immunoglobulin fold / structural protein / TP901-1 ORF46 and ORF49 / phage baseplate
Function / homology
Function and homology information


virus tail, baseplate
Similarity search - Function
Immunoglobulin-like - #3350 / Baseplate upper protein, immunoglobulin like domain / Baseplate upper protein immunoglobulin like domain / BppU, N-terminal / BppU N-terminal domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesLactococcus phage TP901-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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
DepositionNov 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF48


Theoretical massNumber of molelcules
Total (without water)14,4431
Polymers14,4431
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.060, 41.060, 54.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein ORF48


Mass: 14443.050 Da / Num. of mol.: 1 / Fragment: ORF48 N-terminus, UNP residues 1-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLYS / References: UniProt: Q9AZ56
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.85 Å3/Da / Density % sol: 33.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein 33 mg/ml, 1.5 M K2HPO4/0.4 M NaH2PO4, 0.2M NaCl, 0.1 M imidazole, pH 8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2011
RadiationMonochromator: mirrors / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. all: 4537 / Num. obs: 4537 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 33
Reflection shellResolution: 2.3→2.5 Å / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 27 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→35.56 Å / Cor.coef. Fo:Fc: 0.8972 / Cor.coef. Fo:Fc free: 0.8536 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 333 7.34 %RANDOM
Rwork0.2348 ---
all0.236 4537 --
obs0.236 4537 --
Displacement parametersBiso mean: 38.16 Å2
Baniso -1Baniso -2Baniso -3
1-6.4638 Å20 Å20 Å2
2--6.4638 Å20 Å2
3----12.9277 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 74 996
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.007951HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.091289HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0325SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes029HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0141HARMONIC5
X-RAY DIFFRACTIONt_it0951HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion20.06
X-RAY DIFFRACTIONt_chiral_improper_torsion0126SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact01040SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.57 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3151 93 7.2 %
Rwork0.3075 1199 -
all0.308 1292 -
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)
10.1546-0.05010.0422-0.03130.02540.0153-0.00030.0003-0.00260.0003-0.0005-0.0001-0.00110.00090.00090.0011-0.0029-0.0065-0.0010.00250.005120.36123.174922.6701
20.1008-0.04960.0406-0.012-0.02820.0590.00060.0012-0.0014-0.0013-0.00060.0004-0.00040.00070-0.0059-0.0029-0.00270.00010.00150.000712.281212.799116.8209
30.0277-0.0078-0.0233-0.0182-0.02120.0123-0.00010.00050.0007-0.00040.0006-0.0014-0.00140.0011-0.0005-0.0032-0.0035-0.0064-0.0011-0.0018-0.000323.919523.301229.6966
40.0281-0.0134-0.090.08420.09820.0735-0.0003-0.00030.001600.00120.0008-0.00020.0004-0.0008-0.00060.0032-0.00810.0027-0.00340.002110.45722.190231.5704
5-0.00560.0033-0.00120.0327-0.04280.0908-0.0010.0010.00050.00050.0008-0.0004-0.0008-0.00020.00020.0050.0015-0.0085-0.0048-0.00150.000117.404116.372932.7817
6-0.00740.00220.12530.01650.0270-0.00050.00120.001-0.00020.0009-0.0009-0.0024-0.0025-0.0004-0.01280.0027-0.00690.00210.0007-0.00046.224817.243921.3842
70.0003-0.00070.00540.00150.016100.0001-0.00130.00140.0009-0.00040.0006-0.0004-0.00020.00030.00080.0011-0.0056-0.0024-0.0018-0.001812.304423.270239.7971
80.01410.02940.00240.0311-0.00710-0.0011-0.00040.00240.00180.0008-0.0017-0.00170.00050.0002-0.00140.0002-0.0053-0.00170.0051-0.000212.407223.732123.5086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - A|15}A1 - 15
2X-RAY DIFFRACTION2{A|16 - A|30}A16 - 30
3X-RAY DIFFRACTION3{A|31 - A|45}A31 - 45
4X-RAY DIFFRACTION4{A|46 - A|58}A46 - 58
5X-RAY DIFFRACTION5{A|64 - A|80}A64 - 80
6X-RAY DIFFRACTION6{A|81 - A|95}A81 - 95
7X-RAY DIFFRACTION7{A|96 - A|110}A96 - 110
8X-RAY DIFFRACTION8{A|111 - A|123}A111 - 123

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