[English] 日本語
Yorodumi
- PDB-6xc1: Crystal structure of bacteriophage T4 spackle and lysozyme in ort... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xc1
TitleCrystal structure of bacteriophage T4 spackle and lysozyme in orthorhombic form
Components
  • Lysozyme
  • Protein spackle
KeywordsHYDROLASE / Lysozyme / spackle
Function / homology
Function and homology information


superinfection exclusion / host cell periplasmic space / 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 ...superinfection exclusion / host cell periplasmic space / 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
Protein spackle / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Lysozyme - #40 / T4-type lysozyme / : / Glycoside hydrolase, family 24 ...Protein spackle / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Lysozyme - #40 / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Pre-baseplate central spike protein Gp5 / Protein spackle
Similarity search - Component
Biological speciesEscherichia virus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsShi, K. / Oakland, J.T. / Kurniawan, F. / Moeller, N.H. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Commun Biol / Year: 2020
Title: Structural basis of superinfection exclusion by bacteriophage T4 Spackle.
Authors: Shi, K. / Oakland, J.T. / Kurniawan, F. / Moeller, N.H. / Banerjee, S. / Aihara, H.
History
DepositionJun 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysozyme
C: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5117
Polymers32,2072
Non-polymers3045
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint13 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.084, 46.172, 129.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Lysozyme / Baseplate central spike complex protein gp5 / Peptidoglycan hydrolase gp5 / Protein Gp5


Mass: 20131.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus T4 / Production host: Escherichia coli (E. coli) / References: UniProt: P16009, lysozyme
#2: Protein Protein spackle


Mass: 12075.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus T4 / Gene: sp, 61.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P39230
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% (w/v) polyethylene glycol 3350, 20% 2-propanol, 0.1 M HEPES-NaOH pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.92→46.17 Å / Num. obs: 19371 / % possible obs: 99.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 38.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.9
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 1295 / CC1/2: 0.357

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6x6o, 1wth

6x6o

1wth


Resolution: 1.92→43.49 Å / SU ML: 0.2427 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 915 4.74 %
Rwork0.1861 18400 -
obs0.1875 19315 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.62 Å2
Refinement stepCycle: LAST / Resolution: 1.92→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 20 119 2062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342007
X-RAY DIFFRACTIONf_angle_d0.56142698
X-RAY DIFFRACTIONf_chiral_restr0.0382292
X-RAY DIFFRACTIONf_plane_restr0.0042349
X-RAY DIFFRACTIONf_dihedral_angle_d20.8004767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-2.020.34471410.30462562X-RAY DIFFRACTION99.01
2.02-2.150.34281430.26242593X-RAY DIFFRACTION99.78
2.15-2.310.24581300.2292617X-RAY DIFFRACTION99.57
2.31-2.550.24771170.20692629X-RAY DIFFRACTION99.53
2.55-2.910.24241200.19662639X-RAY DIFFRACTION99.28
2.92-3.670.22331260.17692636X-RAY DIFFRACTION98.36
3.67-43.490.16771380.1572724X-RAY DIFFRACTION96.4
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.361124431414.13486580875-0.5954798455398.36148063670.1107747198330.868745183216-0.198006374455-0.08374194860530.0651468175527-0.761071621549-0.125719760915-0.0646226999669-0.1219607685260.1468040357540.335081351640.436038672580.0348335038478-0.02196042003130.348810811402-0.002515765409780.23721638558517.565121944714.41079754417.4307174921
20.971935160451.158451765860.9368479628653.222429334383.814420295962.16975015276-0.3519700227730.2567099629280.197583113961-1.031643000170.0622218816310.231869297326-1.009254600160.1723250712160.1850699751550.568964875814-0.0482123047041-0.1054909360670.360748467890.02407720309090.2993116646498.752267954370.03260489426263.03334920953
38.878089739197.813748507813.418590318177.486274455672.140333370758.671560609770.0579692683314-0.4205411110460.8832656757710.319150289571-0.2885801569631.04658524448-0.490345096853-0.7839614584370.1999416856640.4120275499140.05608833053920.05205510501960.417720220264-0.09940805432470.4791816712677.322816498539.8758843437430.4348246793
46.258580318575.95831873738-4.298286921039.23223559433-5.470319469446.40818423460.379454647003-0.327265809465-0.2161848673210.723490158649-0.5170562619-0.311387190652-0.201134899689-0.3123423847150.1303597834150.3499862566340.00188035570317-0.02941014373320.450444663889-0.0301728406610.26693043423112.7406762416-3.6339700801230.7329116469
56.07701092045.9670607454-6.102430957696.1170759277-6.117584501646.361015129280.0161436793967-0.0577376641018-0.2674758673180.4398433831810.201554046561-0.2443763587630.0563224041718-0.0792203806206-0.1395523348190.3568343966640.00326875458068-0.04572875130350.4333518999010.005061536681610.37763687141715.469014868-11.342108622722.9997070954
69.82740036763-0.489420698472-6.642942578467.490131983043.176255142027.016380272570.2151187746810.0324579530378-0.0979120851224-0.0833847009204-0.3126347807380.473483083189-0.423563538301-0.4697117824990.1121290324950.3820220993750.0438890595763-0.06511062198270.394725506578-0.0122827112250.2785932198035.311216632982.7387496323223.8548661893
75.09767635655-4.5665795707-3.81412824678.915005840581.224247101183.9971825816-0.1132159250960.614781025607-0.563594836579-0.291039306967-0.2805466289870.5755611622040.915895339208-0.9161192662010.4457719496190.374974175513-0.0861306926649-0.0542067479520.414094204864-0.04902370577390.3124837955895.63264736764-8.4694067969621.013968375
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 175 through 237 )AA175 - 2371 - 64
22chain 'A' and (resid 238 through 341 )AA238 - 34165 - 169
33chain 'C' and (resid 23 through 36 )CE23 - 361 - 15
44chain 'C' and (resid 37 through 55 )CE37 - 5516 - 35
55chain 'C' and (resid 56 through 70 )CE56 - 7036 - 50
66chain 'C' and (resid 71 through 86 )CE71 - 8651 - 67
77chain 'C' and (resid 87 through 98 )CE87 - 9868 - 79

+
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://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