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- PDB-9fko: Arm segment of bacteriophage phi812 -

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Basic information

Entry
Database: PDB / ID: 9fko
TitleArm segment of bacteriophage phi812
Components
  • Baseplate protein
  • Unknown peptide
KeywordsVIRUS / phage / arm segment
Function / homologyBaseplate protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsSiborova, M. / Baska, R. / Binovsky, J. / Plevka, P.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: To Be Published
Title: Cell attachment and tail contraction of S. aureus phage phi812
Authors: Binovsky, J. / Siborova, M. / Plevka, P.
History
DepositionJun 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baseplate protein
B: Baseplate protein
C: Baseplate protein
D: Baseplate protein
E: Baseplate protein
F: Baseplate protein
G: Unknown peptide


Theoretical massNumber of molelcules
Total (without water)116,6577
Polymers116,6577
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baseplate protein
C: Baseplate protein
F: Baseplate protein
G: Unknown peptide

A: Baseplate protein


Theoretical massNumber of molelcules
Total (without water)77,9765
Polymers77,9765
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
3
D: Baseplate protein

E: Baseplate protein


Theoretical massNumber of molelcules
Total (without water)38,6812
Polymers38,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y+1/2,-z+21
Buried area2600 Å2
ΔGint-19 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.930, 75.140, 94.450
Angle α, β, γ (deg.)90.000, 109.870, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Baseplate protein


Mass: 19340.623 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 812 (virus)
Gene: 812_119, 812_121, 812a_121, 812F1_121, K1/420_121, K1_121
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1WGQ5
#2: Protein/peptide Unknown peptide


Mass: 613.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.67 Å3/Da / Density % sol: 53.98 % / Description: thick needles
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M LiCl, 0.1 M Tris (pH=7.5), 25 % w/v PEG 4 000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.8233 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2018
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8233 Å / Relative weight: 1
ReflectionResolution: 1.797→46.49 Å / Num. obs: 109412 / % possible obs: 96.07 % / Redundancy: 2.6 % / Biso Wilson estimate: 38.12 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 3.04
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 8201

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→46.49 Å / SU ML: 0.294 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2753 5471 5 %
Rwork0.2452 103940 -
obs0.2467 109411 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8184 0 35 20 8239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01128392
X-RAY DIFFRACTIONf_angle_d1.146311416
X-RAY DIFFRACTIONf_chiral_restr0.06621303
X-RAY DIFFRACTIONf_plane_restr0.01231470
X-RAY DIFFRACTIONf_dihedral_angle_d7.3041110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.42921120.44312133X-RAY DIFFRACTION59.23
1.82-1.840.40821450.37392763X-RAY DIFFRACTION77.28
1.84-1.860.38611530.34132895X-RAY DIFFRACTION80.76
1.86-1.890.36091620.31843088X-RAY DIFFRACTION85.8
1.89-1.910.33291690.29863213X-RAY DIFFRACTION90.16
1.91-1.940.33141790.29423404X-RAY DIFFRACTION94.09
1.94-1.960.32051830.29523470X-RAY DIFFRACTION97.08
1.96-1.990.33511870.31273545X-RAY DIFFRACTION98.86
1.99-2.020.36971880.33153570X-RAY DIFFRACTION99.16
2.02-2.060.36451870.3133562X-RAY DIFFRACTION99.52
2.06-2.090.29871890.29823589X-RAY DIFFRACTION99.84
2.09-2.130.35541870.29513559X-RAY DIFFRACTION100
2.13-2.170.34021910.28973617X-RAY DIFFRACTION100
2.17-2.220.32431910.28633635X-RAY DIFFRACTION100
2.22-2.260.31571880.273574X-RAY DIFFRACTION100
2.26-2.320.29091870.27413549X-RAY DIFFRACTION100
2.32-2.370.31021900.27783622X-RAY DIFFRACTION100
2.38-2.440.32361910.29013622X-RAY DIFFRACTION100
2.44-2.510.32871900.29843613X-RAY DIFFRACTION100
2.51-2.590.33681880.29573574X-RAY DIFFRACTION100
2.59-2.680.33081910.28463629X-RAY DIFFRACTION100
2.68-2.790.33671900.29553606X-RAY DIFFRACTION100
2.79-2.920.31381890.29323594X-RAY DIFFRACTION100
2.92-3.070.33391900.29743602X-RAY DIFFRACTION100
3.07-3.270.33211920.27713650X-RAY DIFFRACTION100
3.27-3.520.28931890.25613596X-RAY DIFFRACTION100
3.52-3.870.24391920.2153635X-RAY DIFFRACTION100
3.87-4.430.21081920.17863654X-RAY DIFFRACTION100
4.43-5.580.17441910.16053634X-RAY DIFFRACTION99.97
5.58-46.490.19521980.18763743X-RAY DIFFRACTION99.82

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