[English] 日本語
Yorodumi
- PDB-7rej: Tailspike protein 4 (TSP4) from phage CBA120, residues 1-335, obt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rej
TitleTailspike protein 4 (TSP4) from phage CBA120, residues 1-335, obtained in the presence of NaK-Tartrate
ComponentsTailspike protein
KeywordsVIRAL PROTEIN / tailspike protein-protein interaction / TSP4 attachment to the tail baseplate / triple beta-helix / beta jellyroll
Function / homologyTail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / IMIDAZOLE / Tailspike protein
Function and homology information
Biological speciesEscherichia virus CBA120
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChao, K. / Shang, X. / Grenfield, J. / Linden, S.B. / Nelson, D.C. / Herzberg, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM110202 United States
CitationJournal: Sci Rep / Year: 2022
Title: Structure of Escherichia coli O157:H7 bacteriophage CBA120 tailspike protein 4 baseplate anchor and tailspike assembly domains (TSP4-N).
Authors: Chao, K.L. / Shang, X. / Greenfield, J. / Linden, S.B. / Alreja, A.B. / Nelson, D.C. / Herzberg, O.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tailspike protein
B: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7804
Polymers72,6422
Non-polymers1382
Water55831
1
A: Tailspike protein
hetero molecules

A: Tailspike protein
hetero molecules

A: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1706
Polymers108,9623
Non-polymers2073
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-y-2,x-y,z1
crystal symmetry operation3_335-x+y-2,-x-2,z1
Buried area18360 Å2
ΔGint-82 kcal/mol
Surface area42300 Å2
MethodPISA
2
B: Tailspike protein
hetero molecules

B: Tailspike protein
hetero molecules

B: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1706
Polymers108,9623
Non-polymers2073
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area15320 Å2
ΔGint-68 kcal/mol
Surface area33140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.030, 78.030, 326.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-512-

HOH

31A-514-

HOH

41B-504-

HOH

51B-510-

HOH

61B-511-

HOH

-
Components

#1: Protein Tailspike protein


Mass: 36320.750 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-335)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus CBA120 / Gene: orf213 / Production host: Escherichia coli (E. coli) / References: UniProt: G3M192
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.8
Details: 1 M potassium sodium tartrate, 0.2 M sodium chloride, 0.1 M imidazole, pH 7.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2018 / Details: mirrors
RadiationMonochromator: double crystal monochromato / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→27.37 Å / Num. obs: 25427 / % possible obs: 98.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 52 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.1
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.85 / Num. unique obs: 2897 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet TSP4-N(1-335) structure

Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 26.051 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.554 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1117 5 %RANDOM
Rwork0.2045 ---
obs0.2056 21436 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.16 Å2 / Biso mean: 80.295 Å2 / Biso min: 29.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å20 Å2
3----2.36 Å2
Refinement stepCycle: final / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 10 31 4322
Biso mean--59.4 51.59 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134392
X-RAY DIFFRACTIONr_bond_other_d0.0060.0173846
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.656016
X-RAY DIFFRACTIONr_angle_other_deg1.5091.5638976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7955573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86424190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.38815629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1941515
X-RAY DIFFRACTIONr_chiral_restr0.090.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.025020
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02861
LS refinement shellResolution: 2.6→2.666 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 64 -
Rwork0.336 1575 -
all-1639 -
obs--98.91 %
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)
11.7202-0.99751.13692.2007-0.11216.4207-0.0835-0.3289-0.03090.5077-0.0547-0.2886-0.17420.40420.13810.3638-0.0621-0.0070.43450.03670.1247-73.825-44.263-70.351
21.84920.6446-0.82814.0637-1.7981.86430.0592-0.3524-0.11940.4554-0.1471-0.3217-0.17370.250.0880.0594-0.0023-0.03350.0994-0.00950.1187-64.813-57.03-25.21
33.4474-0.4274-0.29897.7702-2.01574.2612-0.049-0.2096-0.03980.4969-0.0069-0.5232-0.0260.21390.0560.5538-0.0231-0.07030.73230.02610.8504-65.155-40.6585.861
42.21250.3028-0.77633.0405-2.37465.682-0.1-0.0520.2078-0.0547-0.1462-0.0775-0.06780.09210.24610.0430.0198-0.02170.0196-0.0060.0401-36.906-18.65-6.404
54.27170.99670.27034.36490.87242.3393-0.14140.9620.2161-1.00440.11390.6012-0.2579-0.27050.02740.28030.0241-0.07490.28440.04870.2333-54.495-13.657-54.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 75
2X-RAY DIFFRACTION2A76 - 256
3X-RAY DIFFRACTION3A265 - 335
4X-RAY DIFFRACTION4B4 - 75
5X-RAY DIFFRACTION5B76 - 255

+
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