[English] 日本語
Yorodumi
- PDB-4o4u: Crystal structure of the vaccine antigen Transferrin Binding Prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o4u
TitleCrystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) mutant Trp-176-Ala from Haemophilus parasuis Hp5
ComponentsTbpB
KeywordsMETAL TRANSPORT / Structure-based vaccine design / transferrin receptor / iron acquisition / host pathogen interaction / surface lipoprotein
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Lipocalin - #240 / Lipocalin - #250 / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B ...Lipocalin - #240 / Lipocalin - #250 / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHaemophilus parasuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsCalmettes, C. / Yu, R.H. / Schryvers, A.B. / Moraes, T.F.
CitationJournal: Infect.Immun. / Year: 2015
Title: Nonbinding site-directed mutants of transferrin binding protein B exhibit enhanced immunogenicity and protective capabilities.
Authors: Frandoloso, R. / Martinez-Martinez, S. / Calmettes, C. / Fegan, J. / Costa, E. / Curran, D. / Yu, R.H. / Gutierrez-Martin, C.B. / Rodriguez-Ferri, E.F. / Moraes, T.F. / Schryvers, A.B.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TbpB
B: TbpB
C: TbpB
D: TbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,6435
Polymers233,5514
Non-polymers921
Water5,368298
1
A: TbpB


Theoretical massNumber of molelcules
Total (without water)58,3881
Polymers58,3881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TbpB


Theoretical massNumber of molelcules
Total (without water)58,3881
Polymers58,3881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TbpB


Theoretical massNumber of molelcules
Total (without water)58,3881
Polymers58,3881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4802
Polymers58,3881
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.030, 135.700, 103.960
Angle α, β, γ (deg.)90.000, 100.050, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
TbpB


Mass: 58387.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parasuis (bacteria) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2UKY5*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium formate, 15% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorDetector: CCD / Date: Feb 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.64→48.393 Å / Num. obs: 64684 / Biso Wilson estimate: 51.31 Å2

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→48.393 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7725 / SU ML: 0.42 / σ(F): 2 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2663 3233 5 %
Rwork0.2139 61424 -
obs0.2164 64657 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.88 Å2 / Biso mean: 34.2387 Å2 / Biso min: 4.44 Å2
Refinement stepCycle: LAST / Resolution: 2.64→48.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15570 0 6 298 15874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315900
X-RAY DIFFRACTIONf_angle_d0.73921428
X-RAY DIFFRACTIONf_chiral_restr0.0492291
X-RAY DIFFRACTIONf_plane_restr0.0022805
X-RAY DIFFRACTIONf_dihedral_angle_d11.6795815
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.64-2.67940.37271420.377626882830100
2.6794-2.72130.40361410.370326852826100
2.7213-2.76590.37161390.350826312770100
2.7659-2.81360.35941420.329826982840100
2.8136-2.86480.37741380.322326372775100
2.8648-2.91980.35881420.286826912833100
2.9198-2.97940.32151410.268126752816100
2.9794-3.04420.29761390.238526472786100
3.0442-3.1150.27021420.225226992841100
3.115-3.19290.26341400.227226532793100
3.1929-3.27920.32241420.238926982840100
3.2792-3.37570.29941410.220526782819100
3.3757-3.48460.32161410.230226882829100
3.4846-3.60910.28811390.24072628276799
3.6091-3.75360.35511300.29962480261092
3.7536-3.92430.27331400.21582643278399
3.9243-4.13110.26741410.188226902831100
4.1311-4.38980.21271410.164726842825100
4.3898-4.72850.18961410.145126922833100
4.7285-5.20380.19131420.135426912833100
5.2038-5.95560.16631410.156126842825100
5.9556-7.4990.25881440.179927372881100
7.499-48.40160.20911440.18132727287199

+
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