+Open data
-Basic information
Entry | Database: PDB / ID: 1al0 | ||||||
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Title | PROCAPSID OF BACTERIOPHAGE PHIX174 | ||||||
Components |
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Keywords | VIRUS / COMPLEX (VIRUS CAPSID PROTEINS) / BACTERIOPHAGE / PROCAPSID / SCAFFOLDING PROTEIN / CHAPERONE / Icosahedral virus | ||||||
Function / homology | Function and homology information viral scaffold assembly and maintenance / viral scaffold / modulation by virus of host process / viral procapsid maturation / Hydrolases; Acting on peptide bonds (peptidases) / T=1 icosahedral viral capsid / viral capsid / peptidase activity / host cell cytoplasm / symbiont entry into host cell ...viral scaffold assembly and maintenance / viral scaffold / modulation by virus of host process / viral procapsid maturation / Hydrolases; Acting on peptide bonds (peptidases) / T=1 icosahedral viral capsid / viral capsid / peptidase activity / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / proteolysis Similarity search - Function | ||||||
Biological species | Enterobacteria phage phiX174 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Rossmann, M.G. / Dokland, T. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Structure of a viral procapsid with molecular scaffolding. Authors: Dokland, T. / McKenna, R. / Ilag, L.L. / Bowman, B.R. / Incardona, N.L. / Fane, B.A. / Rossmann, M.G. #1: Journal: Structure / Year: 1995 Title: DNA Packaging Intermediates of Bacteriophage Phi X174 Authors: Ilag, L.L. / Olson, N.H. / Dokland, T. / Music, C.L. / Cheng, R.H. / Bowen, Z. / McKenna, R. / Rossmann, M.G. / Baker, T.S. / Incardona, N.L. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Analysis of the Single-Stranded DNA Bacteriophage Phi X174, Refined at a Resolution of 3.0 A Authors: McKenna, R. / Ilag, L.L. / Rossmann, M.G. #3: Journal: Nature / Year: 1992 Title: Atomic Structure of Single-Stranded DNA Bacteriophage Phi X174 and its Functional Implications Authors: McKenna, R. / Xia, D. / Willingmann, P. / Ilag, L.L. / Krishnaswamy, S. / Rossmann, M.G. / Olson, N.H. / Baker, T.S. / Incardona, N.L. #4: Journal: The Bacteriophages (The Viruses) / Year: 1988 Title: Biology of the Bacteriophage PhiX174 Authors: Hayashi, M. / Aoyama, A. / Delwood, L. / Richardson, D.L. / Hayashi, M.N. #5: Journal: Nature / Year: 1977 Title: Nucleotide Sequence of Bacteriophage Phi X174 DNA Authors: Sanger, F. / Air, G.M. / Barrell, B.G. / Brown, N.L. / Coulson, A.R. / Fiddes, J.C. / Hutchison, C.A. / Slocombe, P.M. / Smith, M. | ||||||
History |
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Remark 285 | THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE ...THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. IN ORDER TO GENERATE THE FULL CRYSTAL AU, APPLY THE FOLLOWING TRANSFORMATION MATRIX OR MATRICES AND SELECTED BIOMT RECORDS TO THE COORDINATES, AS SHOWN BELOW. X0 1 1.000000 0.000000 0.000000 188.08200 X0 2 0.000000 1.000000 0.000000 188.08200 X0 3 0.000000 0.000000 1.000000 188.08200 X1 1 0.834253 0.463850 -0.298103 -4.02480 X1 2 -0.298103 0.834253 0.463850 -4.02480 X1 3 0.463850 -0.298103 0.834253 -4.02480 CRYSTAL AU = (X0) * (BIOMT 1-20) * CHAINS 1,2,3,4,F,G,B + (X1) * (BIOMT 1-20) * CHAINS 1,2,3,4,F,G,B |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1al0.cif.gz | 219.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1al0.ent.gz | 169.2 KB | Display | PDB format |
PDBx/mmJSON format | 1al0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/1al0 ftp://data.pdbj.org/pub/pdb/validation_reports/al/1al0 | HTTPS FTP |
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-Related structure data
Related structure data | 1phxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 | x 20
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 16953.316 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Strain: C / References: UniProt: P69486 #2: Protein | | Mass: 48423.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Strain: C / References: UniProt: P03641 #3: Protein | | Mass: 19061.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Strain: C / References: UniProt: P03643 #4: Protein | | Mass: 13863.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Strain: C / References: UniProt: P03633 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 22 |
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-Sample preparation
Crystal grow | Method: vapor diffusion / pH: 6 Details: PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→45 Å / Num. obs: 527445 / % possible obs: 55.3 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.247 / Rsym value: 0.247 |
Reflection | *PLUS Num. all: 1072459 / Num. measured all: 1646040 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PHX Resolution: 3.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 3.5→8 Å
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.64 Å / Total num. of bins used: 8 /
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Xplor file |
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