[English] 日本語
Yorodumi
- PDB-8ajy: Ruminococcus flavefaciens Cohesin-Dockerin structure: dockerin fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ajy
TitleRuminococcus flavefaciens Cohesin-Dockerin structure: dockerin from ScaH adaptor scaffoldin in complex with the cohesin from ScaE anchoring scaffoldin
Components
  • Cell-wall anchoring protein
  • Dockerin from ScaH
KeywordsPROTEIN BINDING / Cellulosome / Cohesin / Dockerin / Ruminococcus flavefaciens
Function / homologyCBM2/CBM3, carbohydrate-binding domain superfamily / carbohydrate binding / membrane / metal ion binding / Cell-wall anchoring protein
Function and homology information
Biological speciesRuminococcus flavefaciens FD-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsAlves, V.D. / Bule, P. / Fontes, C.M.G.A. / Carvalho, A.L.M. / Najmudin, S. / Duarte, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT) United Kingdom
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structure-function studies can improve binding affinity of cohesin-dockerin interactions for multi-protein assemblies.
Authors: Duarte, M. / Alves, V.D. / Correia, M. / Caseiro, C. / Ferreira, L.M.A. / Romao, M.J. / Carvalho, A.L. / Najmudin, S. / Bayer, E.A. / Fontes, C.M.G.A. / Bule, P.
History
DepositionJul 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 31, 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: Cell-wall anchoring protein
B: Dockerin from ScaH
C: Cell-wall anchoring protein
D: Dockerin from ScaH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,31025
Polymers67,6364
Non-polymers1,67321
Water7,710428
1
A: Cell-wall anchoring protein
B: Dockerin from ScaH
hetero molecules


  • defined by author&software
  • Evidence: isothermal titration calorimetry, The biological assembly is a dimer, formed by a cohesin (Coh) molecule bound to a dockerin (Doc) molecule. The asymmetric unit contains two biological ...Evidence: isothermal titration calorimetry, The biological assembly is a dimer, formed by a cohesin (Coh) molecule bound to a dockerin (Doc) molecule. The asymmetric unit contains two biological assemblies: chains A(Coh)+B(Doc) and C(Coh)+D(Doc)
  • 34.8 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)34,79914
Polymers33,8182
Non-polymers98112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-134 kcal/mol
Surface area13080 Å2
MethodPISA
2
C: Cell-wall anchoring protein
D: Dockerin from ScaH
hetero molecules


  • defined by author&software
  • Evidence: isothermal titration calorimetry, The biological assembly is a dimer, formed by a cohesin (Coh) molecule bound to a dockerin (Doc) molecule. The asymmetric unit contains two biological ...Evidence: isothermal titration calorimetry, The biological assembly is a dimer, formed by a cohesin (Coh) molecule bound to a dockerin (Doc) molecule. The asymmetric unit contains two biological assemblies: chains A(Coh)+B(Doc) and C(Coh)+D(Doc)
  • 34.5 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)34,51111
Polymers33,8182
Non-polymers6939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-81 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.810, 120.000, 65.950
Angle α, β, γ (deg.)90.000, 97.770, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Cell-wall anchoring protein


Mass: 21637.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Gene: scaE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AEF6
#2: Protein Dockerin from ScaH


Mass: 12180.369 Da / Num. of mol.: 2 / Mutation: G79A, R80A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 4 types, 449 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5 and 30% w/v Polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873127 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873127 Å / Relative weight: 1
ReflectionResolution: 1.71→65.344 Å / Num. obs: 66981 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.061 / Rrim(I) all: 0.124 / Net I/σ(I): 8
Reflection shellResolution: 1.714→1.743 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3283 / CC1/2: 0.789 / Rpim(I) all: 0.308 / Rrim(I) all: 0.59 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROC1.1.7data reduction
autoPROC1.1.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IU2

4iu2


Resolution: 1.71→65.34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.414 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 3334 5 %RANDOM
Rwork0.1939 ---
obs0.1961 63640 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.31 Å2 / Biso mean: 18.864 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å2-0.23 Å2
2--1.43 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 1.71→65.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 83 428 4807
Biso mean--43.73 24.38 -
Num. residues----569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134445
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164001
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.6426046
X-RAY DIFFRACTIONr_angle_other_deg1.5241.5939241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11424.641209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49115679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2661512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025079
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
LS refinement shellResolution: 1.714→1.758 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 223 -
Rwork0.27 4677 -
all-4900 -
obs--99.43 %
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)
10.8474-0.02210.22350.64960.17632.48240.00760.1326-0.0012-0.1011-0.0075-0.0229-0.01740.0779-0.00010.06650.00230.0230.0393-0.00350.03779.15072.38910.7336
22.4535-0.3595-0.33351.7966-0.62432.124-0.0408-0.3099-0.05010.18480.04370.0470.0872-0.0326-0.00290.073-0.01070.01460.0803-0.00590.0067-2.0731.874424.6996
30.99340.0717-0.07341.10210.36591.8610.028-0.1793-0.02950.2253-0.0251-0.09540.05430.041-0.00290.1137-0.0147-0.01210.04070.00380.08926.2247-26.1942-2.3425
42.23640.48290.02532.3001-0.63222.1022-0.04580.2640.0654-0.2740.04120.0463-0.0351-0.03010.00460.09030.00590.00550.0528-0.00550.0517-4.8801-27.6394-25.9634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 202
2X-RAY DIFFRACTION2B27 - 110
3X-RAY DIFFRACTION3C1 - 199
4X-RAY DIFFRACTION4D27 - 110

+
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