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- PDB-4eqq: Structure of Ltp, a superinfection exclusion protein from the Str... -

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Basic information

Entry
Database: PDB / ID: 4eqq
TitleStructure of Ltp, a superinfection exclusion protein from the Streptococcus thermophilus temperate phage TP-J34
ComponentsPutative host cell surface-exposed lipoprotein
KeywordsPROTEIN BINDING / HTH fold / superinfection exclusion / lipoprotein ektodomain
Function / homology
Function and homology information


Putative host cell surface-exposed lipoprotein Ltp-like, HTH region / Host cell surface-exposed lipoprotein / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Putative host cell surface-exposed lipoprotein
Similarity search - Component
Biological speciesStreptococcus phage TP-J34 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsBebeacua, C. / Lorenzo, C. / Blangy, S. / Spinelli, S. / Heller, K. / Cambillau, C.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: X-ray structure of a superinfection exclusion lipoprotein from phage TP-J34 and identification of the tape measure protein as its target.
Authors: Bebeacua, C. / Lorenzo Fajardo, J.C. / Blangy, S. / Spinelli, S. / Bollmann, S. / Neve, H. / Cambillau, C. / Heller, K.J.
History
DepositionApr 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Putative host cell surface-exposed lipoprotein
B: Putative host cell surface-exposed lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28314
Polymers24,1372
Non-polymers1,14612
Water5,783321
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-108 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.770, 82.770, 100.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative host cell surface-exposed lipoprotein


Mass: 12068.291 Da / Num. of mol.: 2
Fragment: Ltp from the Streptococcus thermophilus temperate phage TP-J34, ektodomain (unp residues 44-142)
Source method: isolated from a genetically manipulated source
Details: GST cleaved, leaving a 8 residues cloning artefact / Source: (gene. exp.) Streptococcus phage TP-J34 (virus) / Gene: Ltp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O48388
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.55 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: The perecipitant liquor contained Ammonium sulfate 1.50M in tri-Sodium citrate 00.15M, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95373 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2012
RadiationMonochromator: mirrors / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 22479 / Num. obs: 22479 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 33.46 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 26.7
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1635 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.05→22.38 Å / Cor.coef. Fo:Fc: 0.9592 / Cor.coef. Fo:Fc free: 0.9538 / SU R Cruickshank DPI: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 1122 5 %RANDOM
Rwork0.1628 ---
all0.1636 22457 --
obs0.1636 22457 99.98 %-
Displacement parametersBiso mean: 37.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.316 Å20 Å20 Å2
2--1.316 Å20 Å2
3----2.632 Å2
Refine analyzeLuzzati coordinate error obs: 0.199 Å
Refinement stepCycle: LAST / Resolution: 2.05→22.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 60 321 1986
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091679HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.942265HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0592SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes055HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0227HARMONIC5
X-RAY DIFFRACTIONt_it01679HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion16.2
X-RAY DIFFRACTIONt_chiral_improper_torsion0210SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact02255SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.15 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2039 146 4.98 %
Rwork0.1805 2786 -
all0.1817 2932 -
obs--99.98 %
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)
10.14150.00010.02640.064-0.06250.11470-0.001-0.00170.0005-0.0010.00260.0016-0.00250.00110.03610.0003-0.01160.02120.00370.028610.222863.02546.8339
200.1823-0.04710.00980.02510.0732-0.00020.0070.00510.0009-0.0033-0.0040.0036-0.00040.00350.017-0.0502-0.0112-0.00160.0016-0.020515.564155.27777.6427
300.0457-0.00550.04890.18220.03490.0001-0.0007-0.0027-0.0018-0.00040.0018-0.0032-0.00070.00030.003-0.0043-0.0085-0.0013-0.04660.00048.087742.053110.482
40.05940.2187-0.04780.135-0.08870.0598-0.00370.00130.00090.015-0.0014-0.0133-0.01770.01220.00510.0692-0.0296-0.0293-0.043-0.0024-0.028613.308849.032416.6696
50.08920.01240.03720.0134-0.21150.01370.00040.0083-0.0026-0.0042-0.00180.0024-0.0135-0.00780.0014-0.01280.02980.00450.02240.0014-0.0101-1.359939.217.1149
60.0002-0.04210.06450.02360.02720.04590.0012-0.0048-0.00820.00650.00440.0088-0.0015-0.0079-0.00570.00880.0210.02990.0005-0.003-0.0144-2.817731.958626.0988
70.0855-0.1233-0.13270.12970.21890.03360.00060.0029-0.01210.0151-0.00090.0088-0.0194-0.01910.00030.01350.05080.0304-0.0015-0.0224-0.0159-3.132640.679824.2888
800.0360.01810.00440.05880.0013-0.00020-0.0034-0.0017-0.00020.00020.0046-0.00260.0004-0.00280.0203-0.01-0.0039-0.02170.0025-0.122514.27120.7851
90.03140.064-0.02670.0001-0.03540.00660.00080.0013-0.0015-0.0023-0.00010.0009-0.00050.0026-0.0007-0.00670.02190.00150.00640.00810.00056.578926.84218.2555
100.170.10750.27380.0669-0.00310.07660.0040.0131-0.01180.01460.01250.00050.0191-0.0092-0.01640.0135-0.00830.0011-0.0417-0.00440.02140.573418.79711.9386
110.2864-0.1068-0.04850.03660.17340.00920.0010.0155-0.0089-0.00080.0019-0.0018-0.0010.0015-0.003-0.01720.03830.01680.0033-0.01140.012415.128427.58815.8637
120.0157-0.277-0.07040.05680.18390.1850.0007-0.0055-0.0016-0.00140.0037-0.0098-0.00450.0037-0.00450.00520.0455-0.0089-0.01420.01420.007516.087532.542926.4143
130.1011-0.0363-0.13270.2189-0.02730.00560.0012-0.0091-0.0020.00340.0074-0.00850.00880.0004-0.00850.01020.0327-0.0057-0.0277-0.00820.015316.506524.301122.5102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|41 - A|45 }A41 - 45
2X-RAY DIFFRACTION2{ A|46 - A|54 }A46 - 54
3X-RAY DIFFRACTION3{ A|55 - A|66 }A55 - 66
4X-RAY DIFFRACTION4{ A|67 - A|93 }A67 - 93
5X-RAY DIFFRACTION5{ A|94 - A|109 }A94 - 109
6X-RAY DIFFRACTION6{ A|110 - A|123 }A110 - 123
7X-RAY DIFFRACTION7{ A|124 - A|142 }A124 - 142
8X-RAY DIFFRACTION8{ B|45 - B|54 }B45 - 54
9X-RAY DIFFRACTION9{ B|55 - B|66 }B55 - 66
10X-RAY DIFFRACTION10{ B|67 - B|93 }B67 - 93
11X-RAY DIFFRACTION11{ B|94 - B|109 }B94 - 109
12X-RAY DIFFRACTION12{ B|110 - B|123 }B110 - 123
13X-RAY DIFFRACTION13{ B|124 - B|142 }B124 - 142

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