[English] 日本語
Yorodumi
- PDB-5k39: THE TYPE II COHESIN DOCKERIN COMPLEX FROM CLOSTRIDIUM THERMOCELLUM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k39
TitleTHE TYPE II COHESIN DOCKERIN COMPLEX FROM CLOSTRIDIUM THERMOCELLUM
Components
  • Cellulosome anchoring protein cohesin region
  • Dockerin module from a protein of unknown function
KeywordsSTRUCTURAL PROTEIN / S-LAYER / SECRETED / CELL WALL / MEMBRANE PROTEIN
Function / homology
Function and homology information


S-layer / cellulose catabolic process / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / S-layer homology domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carboxypeptidase-like, regulatory domain superfamily ...Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / S-layer homology domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carboxypeptidase-like, regulatory domain superfamily / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Ig domain protein group 2 domain protein / Cell surface glycoprotein 2
Similarity search - Component
Biological speciesRuminiclostridium thermocellum 27405 (bacteria)
Clostridium thermocellum 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsViegas, A. / Pinheiro, B. / Bras, J.L.A. / Romao, M.J. / Alves, V. / Carvalho, A.L. / Fontes, C.M.G.A.
CitationJournal: Sci Rep / Year: 2016
Title: Diverse specificity of cellulosome attachment to the bacterial cell surface.
Authors: Bras, J.L. / Pinheiro, B.A. / Cameron, K. / Cuskin, F. / Viegas, A. / Najmudin, S. / Bule, P. / Pires, V.M. / Romao, M.J. / Bayer, E.A. / Spencer, H.L. / Smith, S. / Gilbert, H.J. / Alves, V. ...Authors: Bras, J.L. / Pinheiro, B.A. / Cameron, K. / Cuskin, F. / Viegas, A. / Najmudin, S. / Bule, P. / Pires, V.M. / Romao, M.J. / Bayer, E.A. / Spencer, H.L. / Smith, S. / Gilbert, H.J. / Alves, V.D. / Carvalho, A.L. / Fontes, C.M.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...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: Cellulosome anchoring protein cohesin region
B: Dockerin module from a protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2734
Polymers37,1932
Non-polymers802
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-29 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.670, 78.630, 35.800
Angle α, β, γ (deg.)90.00, 95.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-339-

HOH

-
Components

#1: Protein Cellulosome anchoring protein cohesin region


Mass: 18947.541 Da / Num. of mol.: 1 / Fragment: COHESION 2 DOMAIN, RESIDUES 205-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum 27405 (bacteria)
Gene: AD2_00639 / Plasmid: pCF1 / Details (production host): altered pET21 plasmid / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0U3TQ90, UniProt: Q06853*PLUS
#2: Protein Dockerin module from a protein of unknown function / Protein CipB dockerin


Mass: 18245.408 Da / Num. of mol.: 1 / Fragment: RESIDUES 2015-2177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum 27405 (bacteria)
Gene: Cthe_1806 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DGE8
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.2 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% (m/v) polyethyleneglycol (PEG) 3350, 4% tacsimate, pH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9735 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.98→39.31 Å / Num. obs: 21909 / % possible obs: 97.8 % / Observed criterion σ(I): 4 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.5 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2MB3 AND 2B59

2mb3

2b59


Resolution: 1.98→18.83 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.842 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24739 2221 10.1 %RANDOM
Rwork0.18702 ---
obs0.19331 19669 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.98→18.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2453 0 2 322 2777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222542
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.9643465
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39225.701107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32115437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.412159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021901
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21138
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21755
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4951.51666
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78722635
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3453998
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0624.5827
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: 1.98→2.031 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 150
Rwork0.189 1420

+
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