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- PDB-5js4: Crystal structure of phiAB6 tailspike -

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Basic information

Entry
Database: PDB / ID: 5js4
TitleCrystal structure of phiAB6 tailspike
ComponentsphiAB6 tailspike
KeywordsVIRAL PROTEIN / viral tailspike / beta-helix / superhelical trimer
Function / homologysymbiont entry into host cell via disruption of host cell glycocalyx / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / symbiont entry into host cell via disruption of host cell envelope / virus tail / Pectin lyase fold / Pectin lyase fold/virulence factor / MALONIC ACID / Tail fiber
Function and homology information
Biological speciesunidentified phage (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsLee, I.M. / Tu, I.F. / Huang, K.F. / Wu, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Sciences and Technology and Academia SinicaNSC101-2923-B-001-005-MY3, MOST104-2325-B-001-003, NSC-101-2319-B-001-003, and MOST105-0210-01-12-01 Taiwan
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage Phi AB6 tailspike protein
Authors: Lee, I.M. / Tu, I.F. / Yang, F.L. / Ko, T.P. / Liao, J.H. / Lin, N.T. / Wu, C.Y. / Ren, C.T. / Wang, A.H. / Chang, C.M. / Huang, K.F. / Wu, S.H.
History
DepositionMay 7, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

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Assembly

Deposited unit
A: phiAB6 tailspike
B: phiAB6 tailspike
C: phiAB6 tailspike
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,20612
Polymers235,2703
Non-polymers9379
Water49,8482767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34310 Å2
ΔGint-174 kcal/mol
Surface area51750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.018, 77.980, 248.080
Angle α, β, γ (deg.)90.00, 100.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1416-

HOH

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Components

#1: Protein phiAB6 tailspike


Mass: 78423.227 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified phage (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A159BDB5*PLUS
#2: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2767 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE DNA AND PROTEIN SEQUENCES HAVE BEEN DEPOSITED IN GENBACK WITH A ACCESSION ...AUTHORS STATE THAT THE DNA AND PROTEIN SEQUENCES HAVE BEEN DEPOSITED IN GENBACK WITH A ACCESSION NUMBER OF KT339321.

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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: 2.81 Å3/Da / Density % sol: 56.18 % / Description: rhombus-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→20 Å / Num. obs: 406268 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 34.3
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3.3 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→19.98 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.63 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15588 19849 5 %RANDOM
Rwork0.13552 ---
obs0.13655 375375 93.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.325 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0.13 Å2
2--0.32 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.48→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12537 0 63 2786 15386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01912870
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211742
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.92817475
X-RAY DIFFRACTIONr_angle_other_deg0.7073.00126952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1551638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11924.712573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.589151998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0011545
X-RAY DIFFRACTIONr_chiral_restr0.0640.21926
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023129
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.3676561
X-RAY DIFFRACTIONr_mcbond_other0.5881.3676560
X-RAY DIFFRACTIONr_mcangle_it0.7722.0548196
X-RAY DIFFRACTIONr_mcangle_other0.7722.0548197
X-RAY DIFFRACTIONr_scbond_it0.771.5156309
X-RAY DIFFRACTIONr_scbond_other0.7691.5146307
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9252.2199279
X-RAY DIFFRACTIONr_long_range_B_refined2.79214.52917681
X-RAY DIFFRACTIONr_long_range_B_other1.69112.27715522
X-RAY DIFFRACTIONr_rigid_bond_restr1.896324612
X-RAY DIFFRACTIONr_sphericity_free27.7835712
X-RAY DIFFRACTIONr_sphericity_bonded6.251526416
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 979 -
Rwork0.18 18769 -
obs--63.53 %

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