[English] 日本語
Yorodumi
- PDB-6hnj: The ligand-bound, open structure of CD0873, a substrate binding p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hnj
TitleThe ligand-bound, open structure of CD0873, a substrate binding protein with adhesive properties from Clostridium difficile.
ComponentsABC-type transport system, sugar-family extracellular solute-binding protein
KeywordsTRANSPORT PROTEIN / Substrate binding protein / adhesin / tyrosine binding protein / lipoprotein
Function / homology
Function and homology information


ABC transporter, substrate-binding protein / ABC transporter substrate binding protein / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / ABC-type transport system, sugar-family extracellular solute-binding protein
Similarity search - Component
Biological speciesPeptoclostridium difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBradshaw, W.J. / Kovacs-Simon, A. / Harmer, N.J. / Michell, S.L. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Molecular features of lipoprotein CD0873: A potential vaccine against the human pathogenClostridioides difficile.
Authors: Bradshaw, W.J. / Bruxelle, J.F. / Kovacs-Simon, A. / Harmer, N.J. / Janoir, C. / Pechine, S. / Acharya, K.R. / Michell, S.L.
History
DepositionSep 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC-type transport system, sugar-family extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5349
Polymers33,9051
Non-polymers6298
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint18 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.963, 57.534, 148.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ABC-type transport system, sugar-family extracellular solute-binding protein


Mass: 33905.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile 630 (bacteria)
Gene: CD630_08730 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18A65
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5, with 2% each of PEG 400, 500 MME, 600, 1000, 2000, 3350, 4000, 5000 MME, 6000, 8000 and 10,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→74.26 Å / Num. obs: 31122 / % possible obs: 99.9 % / Redundancy: 19.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.077 / Rrim(I) all: 0.25 / Net I/σ(I): 7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 20 % / Rmerge(I) obs: 1.483 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1758 / CC1/2: 0.721 / Rpim(I) all: 0.483 / Rrim(I) all: 1.561 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→74.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.83 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23898 1546 5 %RANDOM
Rwork0.20414 ---
obs0.20593 29490 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.663 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å20 Å2
2--0.12 Å2-0 Å2
3----2.81 Å2
Refinement stepCycle: 1 / Resolution: 1.8→74.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 41 143 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022299
X-RAY DIFFRACTIONr_bond_other_d0.0020.022242
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.993100
X-RAY DIFFRACTIONr_angle_other_deg0.93435255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8585304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.95627.83183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62415421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.866151
X-RAY DIFFRACTIONr_chiral_restr0.0860.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02362
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9042.8011195
X-RAY DIFFRACTIONr_mcbond_other1.8952.7981194
X-RAY DIFFRACTIONr_mcangle_it2.8464.1881494
X-RAY DIFFRACTIONr_mcangle_other2.8474.1921495
X-RAY DIFFRACTIONr_scbond_it2.883.3111104
X-RAY DIFFRACTIONr_scbond_other2.8773.3111104
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5574.7281603
X-RAY DIFFRACTIONr_long_range_B_refined5.88134.3482447
X-RAY DIFFRACTIONr_long_range_B_other5.86534.2342428
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 110 -
Rwork0.383 2099 -
obs--99.55 %

+
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