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- PDB-3rwn: Atomic structure of bacteriophage sf6 tail needle knob -

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Basic information

Entry
Database: PDB / ID: 3rwn
TitleAtomic structure of bacteriophage sf6 tail needle knob
ComponentsGene 9 protein
KeywordsVIRAL PROTEIN / Knob / Cell membrane penetration / bacteriophage Sf6
Function / homology
Function and homology information


Sf6-type phage tail needle knob / Sf6-type phage tail needle knob superfamily / Sf6-type phage tail needle knob or tip of some Caudovirales / Sf6-type phage tail needle knob / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLUTAMIC ACID / PHOSPHATE ION / Gene 9 protein
Similarity search - Component
Biological speciesShigella phage Sf6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1 Å
AuthorsBhardwaj, A. / Cingolani, G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Atomic structure of bacteriophage Sf6 tail needle knob.
Authors: Bhardwaj, A. / Molineux, I.J. / Casjens, S.R. / Cingolani, G.
History
DepositionMay 9, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionJun 8, 2011ID: 3JR0
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
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: Gene 9 protein
B: Gene 9 protein
C: Gene 9 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9577
Polymers51,4213
Non-polymers5364
Water18,3211017
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-30 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.407, 88.325, 89.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 130:282 ) and (not element H)
211chain B and (resseq 130:282 ) and (not element H)
311chain C and (resseq 130:282 ) and (not element H)

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Components

#1: Protein Gene 9 protein


Mass: 17140.303 Da / Num. of mol.: 3 / Fragment: unp residues 132-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf6 (virus) / Plasmid: pMAL-2ce / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) plyse / References: UniProt: Q716G6
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1017 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% PEG 3350, 50 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 10, 2010
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1→15 Å / Num. obs: 222826 / % possible obs: 90.1 % / Redundancy: 4.2 % / Rsym value: 0.059 / Net I/σ(I): 25.9
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.3 % / Rsym value: 0.573 / % possible all: 71.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1→14.992 Å / SU ML: 0.07 / σ(F): 0 / Phase error: 13.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1418 3486 89 %
Rwork0.1328 --
obs0.1329 222826 81.88 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 108.829 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4858 Å20 Å2-0 Å2
2--0.7572 Å20 Å2
3----1.243 Å2
Refinement stepCycle: LAST / Resolution: 1→14.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 35 1017 4518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053559
X-RAY DIFFRACTIONf_angle_d1.1634851
X-RAY DIFFRACTIONf_dihedral_angle_d11.3831250
X-RAY DIFFRACTIONf_chiral_restr0.072614
X-RAY DIFFRACTIONf_plane_restr0.005608
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1149X-RAY DIFFRACTIONPOSITIONAL
12B1149X-RAY DIFFRACTIONPOSITIONAL0.385
13C1146X-RAY DIFFRACTIONPOSITIONAL0.475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0004-1.01410.2935760.27878853X-RAY DIFFRACTION46
1.0141-1.02860.2349920.259710556X-RAY DIFFRACTION56
1.0286-1.04390.24651060.260411785X-RAY DIFFRACTION62
1.0439-1.06020.22251180.223912486X-RAY DIFFRACTION66
1.0602-1.07760.23391270.203313418X-RAY DIFFRACTION70
1.0776-1.09620.22341170.1913990X-RAY DIFFRACTION73
1.0962-1.11610.16251140.161414291X-RAY DIFFRACTION75
1.1161-1.13760.15671230.148714773X-RAY DIFFRACTION77
1.1376-1.16080.18471430.14215059X-RAY DIFFRACTION79
1.1608-1.1860.14441440.13815368X-RAY DIFFRACTION81
1.186-1.21360.14661350.131615644X-RAY DIFFRACTION82
1.2136-1.24390.14691510.132615936X-RAY DIFFRACTION84
1.2439-1.27750.17121530.129916195X-RAY DIFFRACTION85
1.2775-1.31510.1311380.125216601X-RAY DIFFRACTION87
1.3151-1.35750.14451430.133916903X-RAY DIFFRACTION88
1.3575-1.4060.14311500.121817041X-RAY DIFFRACTION90
1.406-1.46230.12061650.113317403X-RAY DIFFRACTION91
1.4623-1.52880.11671560.105317677X-RAY DIFFRACTION93
1.5288-1.60930.1051550.101217893X-RAY DIFFRACTION94
1.6093-1.710.12121730.114417650X-RAY DIFFRACTION93
1.71-1.84180.11671520.109718174X-RAY DIFFRACTION95
1.8418-2.02670.11651720.112718327X-RAY DIFFRACTION96
2.0267-2.31910.11121690.111918654X-RAY DIFFRACTION98
2.3191-2.91820.1361650.122918584X-RAY DIFFRACTION98
2.9182-14.99330.15381490.150916876X-RAY DIFFRACTION89

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