[English] 日本語
Yorodumi
- PDB-2ibl: Crystal structure of a helper molecule (HT-mf-thromb) based on mi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ibl
TitleCrystal structure of a helper molecule (HT-mf-thromb) based on mini-fibritin (mf) crystal structure (pdb:1OX3).
ComponentsFibritin
KeywordsCHAPERONE / mini-fibritin / foldon / trimerization / bacteriophage t4 / helper molecule
Function / homology6-Phosphogluconate Dehydrogenase, domain 3 / Fibritin C-terminal / Fibritin C-terminal region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / virion component / Up-down Bundle / Mainly Alpha / Fibritin / Fibritin
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
Enterobacteria phage Ox2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsBoudko, S.P. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The Coiled-coil Domain Structure of the Sin Nombre Virus Nucleocapsid Protein.
Authors: Boudko, S.P. / Kuhn, R.J. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Structure formation in the C terminus of type III collagen guides disulfide cross-linking
Authors: Boudko, S.P. / Engel, J.
#2: Journal: J.Mol.Biol. / Year: 2004
Title: Design and crystal structure of bacteriophage T4 mini-fibritin NCCF
Authors: Boudko, S.P. / Strelkov, S.V. / Engel, J. / Stetefeld, J.
History
DepositionSep 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_name_com.name / _struct_ref.pdbx_align_begin ..._entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibritin


Theoretical massNumber of molelcules
Total (without water)14,0621
Polymers14,0621
Non-polymers00
Water3,549197
1
A: Fibritin

A: Fibritin

A: Fibritin


Theoretical massNumber of molelcules
Total (without water)42,1853
Polymers42,1853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area10590 Å2
ΔGint-85 kcal/mol
Surface area15900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.677, 53.677, 106.458
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-262-

HOH

21A-263-

HOH

31A-264-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: x,y,z; -x+y+1,-x,z; -y,x-y-1,z

-
Components

#1: Protein Fibritin / Collar protein / Whisker antigen control protein


Mass: 14061.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Enterobacteria phage Ox2 (virus)
Gene: wac / Plasmid: pET23d(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10104, UniProt: Q38650
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 30% PEG 400, 0.1 M TrisHCl, 0.2 M magnesium chloride, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.00465 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2005
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00465 Å / Relative weight: 1
ReflectionResolution: 1.32→35 Å / Num. all: 40437 / Num. obs: 40028 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 31.7
Reflection shellResolution: 1.32→1.354 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2823 / Rsym value: 0.216 / % possible all: 89.71

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OX3

1ox3


Resolution: 1.32→35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.972 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.041 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17 2001 5 %RANDOM
Rwork0.16 ---
all0.161 39993 --
obs0.161 39993 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.117 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.32→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 0 197 1030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022867
X-RAY DIFFRACTIONr_bond_other_d0.0010.02589
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.9761178
X-RAY DIFFRACTIONr_angle_other_deg0.82531452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8165107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65625.36641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49915155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.487156
X-RAY DIFFRACTIONr_chiral_restr0.0580.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02157
X-RAY DIFFRACTIONr_nbd_refined0.210.2150
X-RAY DIFFRACTIONr_nbd_other0.180.2608
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2429
X-RAY DIFFRACTIONr_nbtor_other0.0790.2456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.233
X-RAY DIFFRACTIONr_mcbond_it1.1211.5705
X-RAY DIFFRACTIONr_mcbond_other0.5441.5219
X-RAY DIFFRACTIONr_mcangle_it1.3492879
X-RAY DIFFRACTIONr_scbond_it2.1263376
X-RAY DIFFRACTIONr_scangle_it2.8344.5299
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 129 -
Rwork0.174 2591 -
obs-2720 89.71 %

+
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