[English] 日本語
Yorodumi
- PDB-2v5i: Structure of the receptor-binding protein of bacteriophage Det7: ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v5i
TitleStructure of the receptor-binding protein of bacteriophage Det7: a podoviral tailspike in a myovirus
ComponentsSALMONELLA TYPHIMURIUM DB7155 BACTERIOPHAGE DET7 TAILSPIKE
KeywordsVIRAL PROTEIN / O-ANTIGEN BINDING AND HYDROLYSIS / BETA-HELIX
Function / homologyPectate Lyase C-like - #20 / Pectate Lyase C-like / 3 Solenoid / Mainly Beta
Function and homology information
Biological speciesBACTERIOPHAGE (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWalter, M. / Fiedler, C. / Grassl, R. / Biebl, M. / Rachel, R. / Hermo-Parrado, X.L. / Llamas-Saiz, A.L. / Seckler, R. / Miller, S. / van Raaij, M.J.
CitationJournal: J.Virol. / Year: 2008
Title: Structure of the Receptor-Binding Protein of Bacteriophage Det7: A Podoviral Tail Spike in a Myovirus.
Authors: Walter, M. / Fiedler, C. / Grassl, R. / Biebl, M. / Rachel, R. / Hermo-Parrado, X.L. / Llamas-Saiz, A.L. / Seckler, R. / Miller, S. / van Raaij, M.J.
History
DepositionJul 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2017Group: Database references / Category: citation / citation_author / Item: _citation.page_last / _citation_author.name
Revision 1.4Dec 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SALMONELLA TYPHIMURIUM DB7155 BACTERIOPHAGE DET7 TAILSPIKE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5032
Polymers59,4801
Non-polymers231
Water14,970831
1
A: SALMONELLA TYPHIMURIUM DB7155 BACTERIOPHAGE DET7 TAILSPIKE
hetero molecules

A: SALMONELLA TYPHIMURIUM DB7155 BACTERIOPHAGE DET7 TAILSPIKE
hetero molecules

A: SALMONELLA TYPHIMURIUM DB7155 BACTERIOPHAGE DET7 TAILSPIKE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,5086
Polymers178,4393
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area30100 Å2
ΔGint-191.5 kcal/mol
Surface area61730 Å2
MethodPQS
Unit cell
Length a, b, c (Å)100.433, 100.433, 330.042
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-1559-

NA

21A-2432-

HOH

31A-2535-

HOH

41A-2617-

HOH

51A-2638-

HOH

-
Components

#1: Protein SALMONELLA TYPHIMURIUM DB7155 BACTERIOPHAGE DET7 TAILSPIKE


Mass: 59479.691 Da / Num. of mol.: 1
Fragment: O-ANTIGEN BINDING AND HYDROLYSIS DOMAIN AND C-TERMINAL INTERTWINED DOMAIN, RESIDUES 150-708
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE (virus) / Strain: DET7 / Description: REGENSBURG SEWAGE, GERMANY / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174 / Variant (production host): DE3
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNEW SEQUENCE, NOT SUBMITTED YET

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 4.5
Details: 10 TO 30 % (W/V) PEG4000, 0.1 M SODIUM CITRATE PH 4.5, 0 TO 15 % (V/V) GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 27, 2004 / Details: SILICON TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. obs: 80189 / % possible obs: 94.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 14.48 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.8 / % possible all: 85.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TSP

1tsp


Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.193 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17 1598 2 %RANDOM
Rwork0.141 ---
obs0.142 78590 94.6 %-
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: 13.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4143 0 1 831 4975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224289
X-RAY DIFFRACTIONr_bond_other_d0.0010.023870
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9555839
X-RAY DIFFRACTIONr_angle_other_deg0.88839021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12325.054184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26415685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3751519
X-RAY DIFFRACTIONr_chiral_restr0.1210.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02828
X-RAY DIFFRACTIONr_nbd_refined0.1960.2705
X-RAY DIFFRACTIONr_nbd_other0.1830.23774
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22123
X-RAY DIFFRACTIONr_nbtor_other0.080.22632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2473
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.2152
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.41822747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43434426
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.66651600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6171413
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: 1.6→1.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 96
Rwork0.186 5136

+
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