[English] 日本語
Yorodumi
- PDB-1k28: The Structure of the Bacteriophage T4 Cell-Puncturing Device -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k28
TitleThe Structure of the Bacteriophage T4 Cell-Puncturing Device
Components
  • BASEPLATE STRUCTURAL PROTEIN GP27
  • TAIL-ASSOCIATED LYSOZYME
KeywordsHYDROLASE/STRUCTURAL PROTEIN / Triple-stranded beta-helix / OB fold / pseudohexamer / T4 tail lysozyme / HUB / gp27-gp5*-gp5C / HYDROLASE-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / symbiont entry into host cell / identical protein binding
Similarity search - Function
Bacteriophage T4, Gp27, baseplate hub, domain 3 / Nucleic acid-binding protein domain / Nuclear Transport Factor 2; Chain: A, - #190 / Phage tail proteins - 2 layer sandwich fold - #40 / Phage tail protein beta-alpha-beta fold - #20 / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 ...Bacteriophage T4, Gp27, baseplate hub, domain 3 / Nucleic acid-binding protein domain / Nuclear Transport Factor 2; Chain: A, - #190 / Phage tail proteins - 2 layer sandwich fold - #40 / Phage tail protein beta-alpha-beta fold - #20 / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / Protein Gp5, N-terminal OB-fold domain / Gp5, C-terminal / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Gp5 C-terminal repeat (3 copies) / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / 3-Layer(bab) Sandwich / Lysozyme - #40 / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Elongation Factor Tu (Ef-tu); domain 3 / Nuclear Transport Factor 2; Chain: A, / Lysozyme / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Pre-baseplate central spike protein Gp5 / Baseplate central spike complex protein gp27
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsKanamaru, S. / Leiman, P.G. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Arisaka, F. / Rossmann, M.G.
CitationJournal: Nature / Year: 2002
Title: Structure of the cell-puncturing device of bacteriophage T4.
Authors: Kanamaru, S. / Leiman, P.G. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Arisaka, F. / Rossmann, M.G.
History
DepositionSep 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Remark 999SEQUENCE THE AUTHORS MAINTAIN THAT THEIR SEQUENCE IS CORRECT.
Remark 600HETEROGEN THE AUTHORS BELIEVE THAT THE K AND PO4 IONS ARE PRESENT INSIDE THE PROTEIN FROM THE ...HETEROGEN THE AUTHORS BELIEVE THAT THE K AND PO4 IONS ARE PRESENT INSIDE THE PROTEIN FROM THE MOMENT IT FOLDS AND ARE PROBABLY A PART OF THE BIOLOGICAL ASSEMBLY.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TAIL-ASSOCIATED LYSOZYME
D: BASEPLATE STRUCTURAL PROTEIN GP27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6764
Polymers109,5422
Non-polymers1342
Water7,008389
1
A: TAIL-ASSOCIATED LYSOZYME
D: BASEPLATE STRUCTURAL PROTEIN GP27
hetero molecules

A: TAIL-ASSOCIATED LYSOZYME
D: BASEPLATE STRUCTURAL PROTEIN GP27
hetero molecules

A: TAIL-ASSOCIATED LYSOZYME
D: BASEPLATE STRUCTURAL PROTEIN GP27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,02912
Polymers328,6276
Non-polymers4026
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area70110 Å2
ΔGint-270 kcal/mol
Surface area101930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)139.261, 139.261, 381.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-585-

K

21A-586-

PO4

31A-586-

PO4

41A-680-

HOH

51A-804-

HOH

61A-821-

HOH

DetailsThe biological assembly is a hexamer generated from the two polypeptides in the asymmetric unit by the operations: -y,x-y,z and -x+y,-x,z

-
Components

#1: Protein TAIL-ASSOCIATED LYSOZYME / PROTEIN GP5


Mass: 64313.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 5 / Plasmid: pET-29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16009, lysozyme
#2: Protein BASEPLATE STRUCTURAL PROTEIN GP27


Mass: 45228.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 27 / Plasmid: pET-29b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P17172
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 12 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.2 %PEG80001reservoir
20.65 MTris1reservoirpH8.5
335 %glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9786, 0.9783, 1.0188, 0.9414
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2001 / Details: bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97831
31.01881
40.94141
ReflectionResolution: 2.9→50 Å / Num. all: 32046 / Num. obs: 31712 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 11.6
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 10.3 / Num. unique all: 1581 / Rsym value: 0.289 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1602 -RANDOM
Rwork0.211 ---
all0.214 32046 --
obs0.214 31712 5.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7221 0 4 389 7614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.82
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.21 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more