[English] 日本語
Yorodumi
- PDB-10ur: Cohesin domain number 4 from gene locus Rcal_0153 of Ruminococcus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 10ur
TitleCohesin domain number 4 from gene locus Rcal_0153 of Ruminococcus callidus, a type 5 cohesin
ComponentsCohesin domain number 4
KeywordsSTRUCTURAL PROTEIN / Cellulosome / cohesin / extracellular / cohesin type 5
Biological speciesRuminococcus callidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSawaya, M.R. / Arbing, M.A. / Clubb, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Mbio / Year: 2026
Title: AlphaFold-driven structural proteomics reveals extensive cellulosome machinery in human ruminococcal symbionts.
Authors: Minor, C. / Takayesu, A. / Arbing, M.A. / Ha, S.M. / Gunsalus, R.P. / Pellegrini, M. / Sawaya, M.R. / Clubb, R.T.
History
DepositionFeb 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cohesin domain number 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0054
Polymers25,9321
Non-polymers733
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.530, 84.480, 118.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1485-

HOH

-
Components

#1: Protein Cohesin domain number 4


Mass: 25932.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus callidus (bacteria) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.29 % / Description: thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: 0.2 M Magnesium formate pH 5.9, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→39.78 Å / Num. obs: 19021 / % possible obs: 94.1 % / Redundancy: 8.3 % / Biso Wilson estimate: 14.25 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.138 / Net I/σ(I): 11.63
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.850.5919760.7680.6481
1.85-1.90.45310640.8550.4931
1.9-1.950.39312020.8730.4261
1.95-2.010.34913610.9190.3721
2.01-2.080.29112990.9640.311
2.08-2.150.26512740.9380.2841
2.15-2.230.2412230.9530.2571
2.23-2.320.211770.9670.2131
2.32-2.430.19811400.9570.2121
2.43-2.550.17310650.9720.1861
2.55-2.680.14910470.9780.1591
2.68-2.850.1369860.970.1461
2.85-3.040.1199380.9810.1281
3.04-3.290.0988630.980.1051
3.29-3.60.0777930.9910.0831
3.6-4.030.0737190.9890.0791
4.03-4.650.0636440.9950.0681
4.65-5.690.0645530.9950.0681
5.69-8.050.0674380.9940.0721
8.05-39.780.0522590.9980.0551

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.78 Å / SU ML: 0.1985 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 1885 9.92 %
Rwork0.1891 17126 -
obs0.1938 19011 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 3 200 1939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221789
X-RAY DIFFRACTIONf_angle_d1.44632442
X-RAY DIFFRACTIONf_chiral_restr0.0816274
X-RAY DIFFRACTIONf_plane_restr0.0053317
X-RAY DIFFRACTIONf_dihedral_angle_d12.688640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.29311010.2692908X-RAY DIFFRACTION65.35
1.85-1.90.22461090.24291043X-RAY DIFFRACTION75.94
1.9-1.960.26431460.21941242X-RAY DIFFRACTION89.78
1.96-2.030.26481270.21151366X-RAY DIFFRACTION98.68
2.04-2.120.25911590.20131373X-RAY DIFFRACTION99.67
2.12-2.210.26081530.1971376X-RAY DIFFRACTION99.48
2.21-2.330.23791530.19851383X-RAY DIFFRACTION99.61
2.33-2.480.24521550.19321390X-RAY DIFFRACTION99.29
2.48-2.670.25221510.18831373X-RAY DIFFRACTION98.51
2.67-2.930.23891550.19411391X-RAY DIFFRACTION99.68
2.93-3.360.23741570.18381412X-RAY DIFFRACTION99.43
3.36-4.230.1921560.15681405X-RAY DIFFRACTION98.3
4.23-39.780.2251630.17251464X-RAY DIFFRACTION98.01

+
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