[English] 日本語
Yorodumi
- PDB-2vnl: MUTANT Y108Wdel OF THE HEADBINDING DOMAIN OF PHAGE P22 TAILSPIKE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vnl
TitleMUTANT Y108Wdel OF THE HEADBINDING DOMAIN OF PHAGE P22 TAILSPIKE C- TERMINally fused to ISOLEUCINE ZIPPER pIIGCN4 (chimera II)
ComponentsBIFUNCTIONAL TAIL PROTEIN, PIIGCN4
KeywordsVIRAL PROTEIN / CHIMERA / HYDROLASE / LATE PROTEIN / PHAGE P22 TAILSPIKE PROTEIN / MUTANT Y108WDEL / HEAD-BINDING DOMAIN / ISOLEUCINE ZIPPER PIIGCN4
Function / homology
Function and homology information


endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / adhesion receptor-mediated virion attachment to host cell / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / virion attachment to host cell
Similarity search - Function
Tailspike Protein; Chain / Phage P22 tailspike-like, N-terminal domain / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesENTEROBACTERIA PHAGE P22 (virus)
SACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMueller, J.J. / Seul, A. / Mueller, G. / Seckler, R. / Heinemann, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Bacteriophage P22 Tailspike: Structure of the Complete Protein and Function of the Interdomain Linker
Authors: Seul, A. / Mueller, J.J. / Andres, D. / Stettner, E. / Heinemann, U. / Seckler, R.
History
DepositionFeb 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BIFUNCTIONAL TAIL PROTEIN, PIIGCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1604
Polymers16,8841
Non-polymers2763
Water2,360131
1
A: BIFUNCTIONAL TAIL PROTEIN, PIIGCN4
hetero molecules

A: BIFUNCTIONAL TAIL PROTEIN, PIIGCN4
hetero molecules

A: BIFUNCTIONAL TAIL PROTEIN, PIIGCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,48112
Polymers50,6523
Non-polymers8299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area15100 Å2
ΔGint-98.4 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.012, 58.012, 156.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

21A-2009-

HOH

31A-2013-

HOH

-
Components

#1: Protein BIFUNCTIONAL TAIL PROTEIN, PIIGCN4 / LATE PROTEIN GP9 / TAILSPIKE PROTEIN


Mass: 16884.090 Da / Num. of mol.: 1 / Fragment: HEAD-BINDING DOMAIN, RESIDUES 2-122 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: AMINO ACIDS 2-122 OF PHAGE P22 TAILSPIKE HAVE BEEN LINKED TO THE ISOLEUCINE ZIPPER PIIGCN4 (LACKING THE N-TERMINAL MET) 123-152
Source: (gene. exp.) ENTEROBACTERIA PHAGE P22 (virus), (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12528
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 109 TO TRP
Sequence detailsMUTATION Y108W PIIGCN4 COMPRISES RESIDUES 1 TO 31 OF GI5542583, CHIMERA II (THIS ENTRY) ...MUTATION Y108W PIIGCN4 COMPRISES RESIDUES 1 TO 31 OF GI5542583, CHIMERA II (THIS ENTRY) (CORRESPONDING TO 123 TO 152)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.1 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOR DIFFUSION, HANGING DROP. PROTEIN: CONC. 9.3 MG/ML,BUFFER 50MM HEPES, PH6.5; RESERVOIR:20% ISOPROPANOL, 0.1M NA-ACETATE, PH4.6, 0.2M CACL2; DROPLET 2 MICROL:2 MICROL.CRYO:30% GLYCEROL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95373
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2006 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17904 / % possible obs: 98.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.5
Reflection shellResolution: 1.8→1.93 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1LKT, 1EBO

1lkt

1ebo


Resolution: 1.8→19.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.404 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE HEAD-BINDING DOMAIN IS FUSED TO THE ISOLEUCINE ZIPPER PIIGCN4. THE BIOLOGICALLY ACTIVE HEAD- BINDING DOMAIN IS A CRYSTALLOGRAPHIC TRIMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 934 5.2 %RANDOM
Rwork0.19 ---
obs0.192 17174 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 18 131 1307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221225
X-RAY DIFFRACTIONr_bond_other_d0.0010.02821
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9551659
X-RAY DIFFRACTIONr_angle_other_deg0.85432035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7155146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04126.16760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98915221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.497154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02211
X-RAY DIFFRACTIONr_nbd_refined0.2020.2249
X-RAY DIFFRACTIONr_nbd_other0.1740.2823
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2610
X-RAY DIFFRACTIONr_nbtor_other0.0850.2599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7222975
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9931217
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9293561
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5974.5442
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.256 94
Rwork0.231 1666

+
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